Production db notclean

.github/workflows/qiita-ci.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         include:
           - cover_package: "qiita_db"
-          - cover_package: "qiita_pet qiita_core qiita_ware"
+        #  - cover_package: "qiita_pet qiita_core qiita_ware"
 
     services:
       postgres:
@@ -57,6 +57,8 @@ jobs:
           # pull out the port so we can modify the configuration file easily
           pgport=${{ job.services.postgres.ports[5432] }}
           sed -i "s/PORT = 5432/PORT = $pgport/" qiita_core/support_files/config_test.cfg
+          # SMJ: set to productive mode!
+          sed -i "s/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/" qiita_core/support_files/config_test.cfg
 
           # PGPASSWORD is read by pg_restore, which is called by the build_db process.
           export PGPASSWORD=postgres
@@ -101,25 +103,7 @@ jobs:
           pwd
           mkdir ~/.qiita_plugins
 
-      - name: Install plugins
-        shell: bash -l {0}
-        run: |
-          wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-linux-conda.yml
-          conda env create --quiet -n qtp-biom --file qiime2-2022.11-py38-linux-conda.yml
-          rm qiime2-2022.11-py38-linux-conda.yml
-          export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt
-          export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
-          export REDBIOM_HOST="http://localhost:7379"
-          conda activate qtp-biom
-          pip install -U pip
-          pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
-          pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip
-
-          # if QIITA_ROOTCA_CERT is appended to certifi's cacert.pem file,
-          # then --server-cert does not need to be specified to any plugin,
-          # including configure_biom.
-          # echo `python -c "import certifi;print(certifi.where())"`
-          configure_biom --env-script "source /home/runner/.profile; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
+      # SMJ: don't install any plugins! ~/.qiita_plugins directory should remain empty
 
       - name: Starting services
         shell: bash -l {0}
@@ -156,84 +140,8 @@ jobs:
           conda activate qiita
           # adapt environment_script for private qiita plugins from travis to github actions.
           sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile; conda #' -i qiita_db/support_files/patches/54.sql
-          qiita-env make --no-load-ontologies
-          qiita-test-install
-          qiita plugins update
-
-          echo "6. Starting supervisord => multiple qiita instances"
-          supervisord -c ${PWD}/qiita_pet/supervisor_example.conf
-          sleep 10
-          cat /tmp/supervisord.log
-
-          echo "7. Starting plugins"
-          conda deactivate
-          conda activate qtp-biom
-          export QIITA_CLIENT_DEBUG_LEVEL=DEBUG
-          start_biom https://localhost:8383 register ignored
-          conda deactivate
-
-          echo "8. Setting up SSH"
-          ssh-keygen -t rsa -b 4096 -N '' -f $PWD/qiita_ware/test/test_data/test_key
-          mkdir ~/.ssh/
-          cp $PWD/qiita_ware/test/test_data/test_key* ~/.ssh/
-          cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys
-          chmod 600 $PWD/qiita_ware/test/test_data/test_key*
-          chmod 600 ~/.ssh/*
-          chmod 700 ~/.ssh/
-          echo "Connecting as $USER@localhost"
-          # this line (and the -o StrictHostKeyChecking=no) is so the server
-          # is added to the list of known servers
-          scp -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1
-
-      - name: Main tests
-        shell: bash -l {0}
-        env:
-          COVER_PACKAGE: ${{ matrix.cover_package }}
-        run: |
-          conda activate qiita
-          export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt
-          export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
-          # for testing we only need to have this set, not actually exist
-          export QIITA_JOB_SCHEDULER_EPILOGUE=`/path/to/epilogue/file`
-          export REDBIOM_HOST="http://localhost:7379"
-
-          nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=${COVER_PACKAGE// / --cover-package=} -e 'test_submit_EBI_parse_EBI_reply_failure' -e 'test_full_submission'
-
-          # killing the qiita server to run the next commands
-          QIITA_PID=`cat /tmp/supervisord.pid`
-          kill $QIITA_PID
-          sleep 10
-          if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then test_data_studies/commands.sh; all-qiita-cron-job; fi
-
-      - name: Submit coveralls
-        uses: AndreMiras/coveralls-python-action@develop
-        with:
-          github-token: ${{ secrets.github_token }}
-          flag-name: "${{ matrix.cover_package }}"
-          parallel: true
-
-  coveralls_finish:
-    needs: main
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: AndreMiras/coveralls-python-action@develop
-      with:
-        github-token: ${{ secrets.github_token }}
-        parallel-finished: true
-
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-    - name: flake8
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.9'
-    - name: install dependencies
-      run: python -m pip install --upgrade pip
-    - name: Check out repository code
-      uses: actions/checkout@v2
-    - name: lint
-      run: |
-        pip install -q flake8
-        flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py
+          qiita-env make #--no-load-ontologies
+
+          PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.software;"
+          PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.default_workflow;"
+

qiita_db/sql_connection.py

@@ -88,12 +88,15 @@ def _open_connection(self):
                     host=qiita_config.host,
                     port=qiita_config.port)
                 self._connection.autocommit = True
+                print("STEFAN:admin", qiita_config.admin_user, qiita_config.admin_password, qiita_config.host, qiita_config.port)
             else:
                 self._connection = connect(user=qiita_config.user,
                                            password=qiita_config.password,
                                            database=qiita_config.database,
                                            host=qiita_config.host,
                                            port=qiita_config.port)
+                print("STEFAN:user", qiita_config.user, qiita_config.password, qiita_config.database, qiita_config.host, qiita_config.port)
+
         except OperationalError as e:
             # catch three known common exceptions and raise runtime errors
             try: