Update test.yml and fix failed tests

.github/workflows/test.yml

@@ -19,139 +19,135 @@
 jobs:
 
   workspace_container_tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.10
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
       - name: Install dependencies and set up test config
         shell: bash
         run: |
           # set up python dependencies
           pip install pytest requests
 
       - name: Run tests
         shell: bash
         run: |
           sh test/run_tests.sh
 
   workspace_deluxe_tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     strategy:
       fail-fast: false
       matrix:
         include:
           - java: '8'  # needs to be compatible so jars can be used w/ java 8
             mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
             minio: '2019-05-23T00-29-34Z'
             wired_tiger: 'true'
             gradle_test: 'testQuick'
           # the current production setup
           - java: '11'
             mongo: 'mongodb-linux-x86_64-3.6.13'
             minio: '2019-05-23T00-29-34Z'
             wired_tiger: 'false'
             gradle_test: 'testQuick'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: ${{matrix.java}}
 
-      - name: Set up Python 3.7  # sample service is on 3.7, handle service is on sdkbase2.latest
-        uses: actions/setup-python@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.7"
+          python-version: "3.9.19"
 
       - name: Install dependencies and set up test config
         shell: bash
         run: |
           export HOMEDIR=`pwd`
 
           # set up python dependencies
           cd python_dependencies
           pip install pipenv
           pipenv sync --system
           cd ..
 
           # move to parent dir of homedir to install binaries etc
           cd ..
 
           # set up arango
           export ARANGODB_VER=3.9.1
           export ARANGODB_V=39
           curl -O https://download.arangodb.com/arangodb$ARANGODB_V/Community/Linux/arangodb3-linux-$ARANGODB_VER.tar.gz
           tar -xf arangodb3-linux-$ARANGODB_VER.tar.gz
           export ARANGO_EXE=$(pwd)/arangodb3-linux-$ARANGODB_VER/bin/arangod
           export ARANGO_JS=$(pwd)/arangodb3-linux-$ARANGODB_VER/usr/share/arangodb3/js/
 
-           # set up handle service
-          export HS_COMMIT=08e18379817e16db920501b66ba62b66598f506c
-          export LOG_COMMIT=b549c557e3c519e0a55eadf7863a93db25cd6806
+          # set up handle service
+          # HS_COMMIT corresponds to Handle Service2 tag v1.0.7
+          export HS_COMMIT=335020d26f3663da456be5afee3cb4b8ed8622f4
           git clone https://github.com/kbase/handle_service2.git
           cd handle_service2/
           git checkout $HS_COMMIT
-          sudo chmod -R 777 .
           cd lib/
-          mkdir biokbase
-          cd biokbase/
-          wget https://raw.githubusercontent.com/kbase/sdkbase2/$LOG_COMMIT/log.py
-          cd ..
           export HSDIR=`pwd`
           cd ../..
 
           # set up sample service
-          export SAMPLE_COMMIT=6813fb148e95db2b11db6eea04f4d1d45cbb7119
+          # SAMPLE_COMMIT corresponds to Sample Service tag v0.2.1
+          export SAMPLE_COMMIT=aa0303c4d5d4aa1e3cf0c9ecb36366fb1127f93e
           git clone https://github.com/kbase/sample_service.git
           cd sample_service
           git checkout $SAMPLE_COMMIT
           cd lib
           export SAMPLE_DIR=`pwd`
           cd ../..
 
           # set up blobstore
           wget -q -O blobstore https://github.com/kbase/blobstore/releases/download/v0.1.2/blobstore_linux_amd64
           chmod a+x blobstore
           export BLOBEXE=$(pwd)/blobstore
 
           # set up mongo
           wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
           tar xfz ${{matrix.mongo}}.tgz
           export MONGOD=`pwd`/${{matrix.mongo}}/bin/mongod
 
           # set up minio
           export MINIO=$HOMEDIR/test_dependencies/minio/${{matrix.minio}}/minio
           gunzip $MINIO.gz 
           chmod a+x $MINIO
 
           # set up test config
           cd $HOMEDIR
           cp -n test.cfg.example test.cfg
           sed -i "s#^test.temp.dir =.*#test.temp.dir=temp_test_dir#" test.cfg
           sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
           sed -i "s#^test.minio.exe.*#test.minio.exe=$MINIO#" test.cfg
           sed -i "s#^test.mongo.useWiredTiger.*#test.mongo.useWiredTiger=${{matrix.wired_tiger}}#" test.cfg
           sed -i "s#^test.blobstore.exe.*#test.blobstore.exe=$BLOBEXE#" test.cfg
           sed -i "s#^test.handleservice.dir.*#test.handleservice.dir=$HSDIR#" test.cfg
           sed -i "s#^test.sampleservice.dir.*#test.sampleservice.dir=$SAMPLE_DIR#" test.cfg
           sed -i "s#^test.arango.exe.*#test.arango.exe=$ARANGO_EXE#" test.cfg
           sed -i "s#^test.arango.js.*#test.arango.js=$ARANGO_JS#" test.cfg
           cat test.cfg
 
       - name: Run tests
         shell: bash
         run: |
           ./gradlew ${{matrix.gradle_test}}
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

python_dependencies/Pipfile

@@ -11,27 +11,31 @@ jsonrpcbase = "==0.2.0"
 requests = "==2.22.0"
 
 # handle service dependencies
-cachetools = "*"
+cachetools = "==4.2.2"
 configparser = "*"
-pymongo = "==3.11.0"
-uwsgi = "==2.0.18"
+pymongo = "==4.7.2"
+uwsgi = "==2.0.22"
 
 # sample service dependencies
 python-arango = "==5.0.0"
-apscheduler = "==3.6.3"
+apscheduler = "==3.9.1"
 maps = "==5.1.1"
 cacheout = "==0.11.2"
 pyyaml = "==5.3"
 jsonschema = "==3.2.0"
-pint = "==0.10.1"
+pint = "==0.17"
 python-ranges = "==0.1.3"
 pygtrie = "==2.3.2"
-jinja2 = "==2.11.2"
-gevent = "==20.5.0"
+jinja2 = "==2.11.3"
+gevent = "==24.11.1"
 gunicorn = "==20.0.4"
 kafka-python = "==2.0.1"
-greenlet = "==0.4.16"
+greenlet = "==3.1.1"
 typing-extensions = "*"
+types-pyyaml = "*"
+types-requests = "*"
+pipenv = "*"
+shell = "*"
 
 [requires]
-python_version = "3.7"
+python_version = "3.9.19"