Merge pull request #11410 from bernt-matthias/topic/fix-configfile-20.05

.ci/minikube-test-setup/deployment.yaml

@@ -0,0 +1,32 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  labels:
+    app.kubernetes.io/name: testing
+  name: testing
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: test
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: test
+    spec:
+      containers:
+      - image: postgres:12
+        name: postgres
+        ports:
+        - containerPort: 5432
+        env:
+          - name: POSTGRES_DB
+            value: postgres
+          - name: POSTGRES_USER
+            value:  postgres
+          - name: POSTGRES_PASSWORD
+            value: postgres
+      - image: rabbitmq
+        name: rabbitmq
+        ports:
+        - containerPort: 5672

.ci/minikube-test-setup/start_services.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -ex
+
+SCRIPTDIR=$(dirname "${BASH_SOURCE[0]}")
+kubectl apply -f "$SCRIPTDIR/deployment.yaml"
+kubectl expose deployment testing --type=LoadBalancer --name=testing-service
+
+CLUSTER_IP=$(kubectl get service testing-service -o jsonpath='{.spec.clusterIP}')
+GALAXY_TEST_DBURI="postgresql://postgres:postgres@${CLUSTER_IP}:5432/galaxy?client_encoding=utf-8"
+GALAXY_TEST_AMQP_URL="amqp://${CLUSTER_IP}:5672)//"
+export GALAXY_TEST_DBURI
+export GALAXY_TEST_AMQP_URL

.github/workflows/integration.yaml

@@ -6,14 +6,15 @@ env:
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
         subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
     services:
       postgres:
-        image: postgres:11
+        image: postgres:13
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
@@ -25,36 +26,48 @@ jobs:
         ports:
           - 5672:5672
     steps:
-    - name: Prune unused docker image, volumes and containers
-      run: docker system prune -a -f
-    - name: Clean dotnet folder for space
-      if: matrix.subset == 'kubernetes'
-      run: rm -Rf /usr/share/dotnet
-    - name: Setup Minikube
-      if: matrix.subset == 'kubernetes'
-      id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.3
-      with:
-        minikube-version: "1.9.0-0_amd64"
-    - name: Launch Minikube
-      if: matrix.subset == 'kubernetes'
-      run: eval ${{ steps.minikube.outputs.launcher }}
-    - name: Check pods
-      if: matrix.subset == 'kubernetes'
-      run: |
-        kubectl get pods
-    - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip dir
-      uses: actions/cache@v1
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Run tests
-      run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy root'
+      - name: Prune unused docker image, volumes and containers
+        run: docker system prune -a -f
+      - name: Clean dotnet folder for space
+        if: matrix.subset == 'kubernetes'
+        run: rm -Rf /usr/share/dotnet
+      - name: Setup Minikube
+        if: matrix.subset == 'kubernetes'
+        id: minikube
+        uses: CodingNagger/minikube-setup-action@v1.0.3
+        with:
+          minikube-version: "1.9.0-0_amd64"
+      - name: Launch Minikube
+        if: matrix.subset == 'kubernetes'
+        run: eval ${{ steps.minikube.outputs.launcher }}
+      - name: Check pods
+        if: matrix.subset == 'kubernetes'
+        run: |
+          kubectl get pods
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v1
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Run tests
+        if: matrix.subset != 'kubernetes'
+        run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
+        working-directory: 'galaxy root'
+      - name: Run tests
+        if: matrix.subset == 'kubernetes'
+        run: |
+          . .ci/minikube-test-setup/start_services.sh
+          ./run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Integration test results (${{ matrix.python-version }}, ${{ matrix.subset }})
+          path: 'galaxy root/run_integration_tests.html'

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -82,7 +82,7 @@ pyparsing = "*"
 "Fabric3" = "*"
 paramiko = "*"
 cloudbridge = "*"
-social_auth_core = {version = "==3.3.0", extras = ['openidconnect']}
+social-auth-core = {version = "==3.3.0", extras = ['openidconnect']}
 cloudauthz = "==0.6.0"
 gxformat2 = "*"
 refgenconf = ">=0.7.0"

lib/galaxy/tools/parameters/wrapped_json.py

@@ -94,10 +94,13 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
     elif input_type == "boolean":
         json_value = _cast_if_not_none(value_wrapper, bool)
     elif input_type == "select":
-        if input.multiple and packaging.version.parse(str(profile)) >= packaging.version.parse('20.05'):
-            json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]
-        else:
+        if packaging.version.parse(str(profile)) < packaging.version.parse('20.05'):
             json_value = _cast_if_not_none(value_wrapper, str)
+        else:
+            if input.multiple:
+                json_value = [str(_) for _ in _cast_if_not_none(value_wrapper.value, list)]
+            else:
+                json_value = _cast_if_not_none(value_wrapper.value, str)
     elif input_type == "data_column":
         # value is a SelectToolParameterWrapper()
         if input.multiple:

packages/data/requirements.txt

@@ -9,7 +9,7 @@ parsley
 numpy<=1.16
 pycryptodome
 pysam
-social_auth_core
+social-auth-core[openidconnect]==3.3.0
 SQLAlchemy
 sqlalchemy-migrate
 sqlalchemy-utils

test/functional/tools/inputs_as_json.xml

@@ -27,8 +27,8 @@ if test_case == "1":
     assert_equals(as_dict["inttest"], 12456)
     assert_equals(as_dict["floattest"], 6.789)
     assert_equals(as_dict["radio_select"], "a_radio")
-    assert_equals(as_dict["optional_select"], None)
-    assert_equals(as_dict["optional_multiple_select"], [])
+    assert_equals(as_dict["optional_select"], "None")
+    assert_equals(as_dict["optional_multiple_select"], "None")
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -43,7 +43,7 @@ elif test_case == "2":
     assert_equals(as_dict["floattest"], 1.0)
     assert_equals(as_dict["radio_select"], "a_radio")
     assert_equals(as_dict["optional_select"], "a")
-    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])
+    assert_equals(as_dict["optional_multiple_select"], 'a,b')
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["cond"]["cond_test"], "second")
     assert_equals(as_dict["cond"]["more_text"], "sdefault")

test/functional/tools/inputs_as_json_profile.xml

@@ -1,7 +1,7 @@
 <!-- test if profile version of inputs json generation works, i.e.
      - multiple selects get comma separated string (lists >= 20.05)
      - empty optional selects get "None" ([] >= 20.05) -->
-<tool id="inputs_as_json" name="inputs_as_json" profile="20.01" version="1.0.0">
+<tool id="inputs_as_json_profile" name="inputs_as_json_profile" profile="20.05" version="1.0.0">
     <command detect_errors="exit_code"><![CDATA[
         cat inputs.json &&
         python $check_inputs inputs.json $test_case
@@ -30,8 +30,8 @@ if test_case == "1":
     assert_equals(as_dict["inttest"], 12456)
     assert_equals(as_dict["floattest"], 6.789)
     assert_equals(as_dict["radio_select"], "a_radio")
-    assert_equals(as_dict["optional_select"], "None")
-    assert_equals(as_dict["optional_multiple_select"], "None")
+    assert_equals(as_dict["optional_select"], None)
+    assert_equals(as_dict["optional_multiple_select"], [])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -46,7 +46,7 @@ elif test_case == "2":
     assert_equals(as_dict["floattest"], 1.0)
     assert_equals(as_dict["radio_select"], "a_radio")
     assert_equals(as_dict["optional_select"], "a")
-    assert_equals(as_dict["optional_multiple_select"], 'a,b')
+    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["cond"]["cond_test"], "second")
     assert_equals(as_dict["cond"]["more_text"], "sdefault")