From dff39af2bfae9930b32806bfd906bdefc2540dc0 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Fri, 2 Feb 2024 17:22:53 -0600 Subject: [PATCH 1/7] Update download_runner.sh --- scripts/download_runner.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/download_runner.sh b/scripts/download_runner.sh index b61b65926..476edf69a 100755 --- a/scripts/download_runner.sh +++ b/scripts/download_runner.sh @@ -4,7 +4,7 @@ set -x runner_dir=/runner mkdir -p ${runner_dir} && cd ${runner_dir} && rm -rf JobRunner -git clone --single-branch --branch ee2 https://github.com/kbase/JobRunner.git +git clone --single-branch --branch main https://github.com/kbase/JobRunner.git rm -rf JobRunner/test -rm -rf Jobrunner/.git +rm -rf JobRunner/.git tar -czvf ${runner_dir}/JobRunner.tgz JobRunner From b1215303f93a09f778b0d675c9115cc9694dc899 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 10:08:19 -0500 Subject: [PATCH 2/7] Bump module version to 0.0.16 --- kbase.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kbase.yml b/kbase.yml index a93ca87de..c0fbf5630 100644 --- a/kbase.yml +++ b/kbase.yml @@ -8,7 +8,7 @@ service-language: python module-version: - 0.0.15 + 0.0.16 owners: - [bsadkhin, tgu2, wjriehl, gaprice] \ No newline at end of file + [bsadkhin, tgu2, wjriehl, gaprice] From 4f8403402eecd4709ccac5cbcd2d0b887962f2cc Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 10:09:14 -0500 Subject: [PATCH 3/7] Add release notes for version 0.0.16 Updated release notes for version 0.0.16 with changes to JobRunner. --- RELEASE_NOTES.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 7c86d2990..5807e74fa 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,6 +1,9 @@ # execution_engine2 (ee2) release notes ========================================= +## 0.0.16 +- Update JobRunner to no longer use ee2 branch (requires sanic==21.12.2 to be installed on the workers) + ## 0.0.15 - Update JobRunner and Execution Engine to substitute internal urls to go through cloudflare From aa7e8e61ed99f113a8b8403ae23a014e9a4c2c3d Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 14:24:46 -0500 Subject: [PATCH 4/7] Attempt to fix failing build --- Dockerfile | 6 +++++- Pipfile | 2 +- requirements.txt | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 76db5f3a8..89c3a9820 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,10 @@ RUN apt-get install -y gcc wget vim htop tmpreaper RUN mkdir -p /etc/apt/sources.list.d # Install condor -RUN curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run + +#RUN curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run + +RUN DEBIAN_FRONTEND=noninteractive apt-get install -y htcondor # Install jars for testing purposes # Uncomment this if you want to run tests inside the ee2 container on MacOSX @@ -38,6 +41,7 @@ ENV PATH=/miniconda-latest/bin:$PATH RUN pip install --upgrade pip && python -V COPY ./requirements.txt /kb/module/requirements.txt + RUN pip install -r /kb/module/requirements.txt RUN adduser --disabled-password --gecos '' -shell /bin/bash kbase # ----------------------------------------- diff --git a/Pipfile b/Pipfile index 8d437ecec..c065dccdf 100644 --- a/Pipfile +++ b/Pipfile @@ -28,7 +28,7 @@ gunicorn = "==20.0.4" h11 = "==0.8.1" h2 = "==3.1.0" hpack = "==3.0.0" -htcondor = "==8.9.8" +htcondor = "==25.2.1" httpcore = "==0.3.0" httptools = "==0.0.13" hyperframe = "==5.2.0" diff --git a/requirements.txt b/requirements.txt index c5b928b43..98f59e615 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ coverage==5.5 docker==5.0.0 gevent==24.2.1 ; python_version >= "3.10" and python_version < "4.0" gunicorn==20.1.0 -htcondor==23.8.1 +htcondor==25.2.1 Jinja2==3.0.1 JSONRPCBase==0.2.0 mock==4.0.3 From 0b2aa7f9b664fba84dda0088b59d8b0c4a02d379 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 14:34:06 -0500 Subject: [PATCH 5/7] Attempt to fix failing build --- .github/workflows/ee2-tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ee2-tests.yml b/.github/workflows/ee2-tests.yml index 41007ff9a..71a351f51 100644 --- a/.github/workflows/ee2-tests.yml +++ b/.github/workflows/ee2-tests.yml @@ -64,6 +64,7 @@ jobs: python-version: "3.10.14" - name: Install dependencies run: | + curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run pip install -r requirements.txt git clone https://github.com/kbase/jars /opt/jars - name: Set MongoDB Version and Init Path From 905825e5363d3f1c80b6d8a680bbed030b423ef1 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 14:41:16 -0500 Subject: [PATCH 6/7] Attempt to fix failing build --- .github/workflows/ee2-tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ee2-tests.yml b/.github/workflows/ee2-tests.yml index 71a351f51..2bbe5d3ca 100644 --- a/.github/workflows/ee2-tests.yml +++ b/.github/workflows/ee2-tests.yml @@ -64,7 +64,9 @@ jobs: python-version: "3.10.14" - name: Install dependencies run: | - curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run + pip install htcondor + pip freeze | grep htcondor + import htcondor; print(htcondor.__version__) pip install -r requirements.txt git clone https://github.com/kbase/jars /opt/jars - name: Set MongoDB Version and Init Path From 26d50121c5e4fc6d1b1ea99faf19b02d44140618 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Wed, 29 Oct 2025 17:45:21 -0500 Subject: [PATCH 7/7] Attempt to fix failing build --- .github/workflows/ee2-tests.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ee2-tests.yml b/.github/workflows/ee2-tests.yml index 2bbe5d3ca..f247392e8 100644 --- a/.github/workflows/ee2-tests.yml +++ b/.github/workflows/ee2-tests.yml @@ -66,7 +66,6 @@ jobs: run: | pip install htcondor pip freeze | grep htcondor - import htcondor; print(htcondor.__version__) pip install -r requirements.txt git clone https://github.com/kbase/jars /opt/jars - name: Set MongoDB Version and Init Path