Merge branch 'dev' into topic/lint-context

.ci/first_startup.sh

@@ -1,16 +1,32 @@
 #!/bin/sh
+case "$1" in
+    galaxy|"")
+        SCRIPT=./run.sh
+        PORT=8080
+        LOGFILE=galaxy.log
+        ;;
+    reports)
+        SCRIPT=./run_reports.sh
+        PORT=9001
+        LOGFILE=reports_webapp.log
+        ;;
+    *)
+        echo "ERROR: Unrecognized app"
+        exit 1
+        ;;
+esac
 TRIES=120
-URL=http://localhost:8080
+URL=http://localhost:$PORT
 EXIT_CODE=1
 i=0
 echo "Testing for correct startup:"
-bash run.sh --daemon && \
+$SCRIPT --daemon && \
     while [ "$i" -le $TRIES ]; do
         curl --max-time 1 "$URL" && EXIT_CODE=0 && break
         sleep 1
         i=$((i + 1))
     done
-bash run.sh --skip-wheels --stop-daemon
+$SCRIPT --skip-wheels --stop-daemon
 echo "exit code:$EXIT_CODE, showing startup log:"
-cat galaxy.log
+cat "$LOGFILE"
 exit $EXIT_CODE

.circleci/config.yml

@@ -27,7 +27,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:3.6
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -85,26 +85,17 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: circleci/python:3.6
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - run: sudo apt-get update
       - run: sudo apt-get install -y libxml2-utils
       - *install_tox
       - run: tox -e validate_test_tools
-  test_galaxy_release:
-    docker:
-      - image: circleci/python:3.6
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - *install_deb_reqs
-      - run: tox -e test_galaxy_release
   test_galaxy_packages:
     docker:
-      - image: circleci/python:3.6
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache

.github/workflows/dependencies.yaml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.6']
+        python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2

.github/workflows/first_startup.yaml

@@ -19,10 +19,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6', '3.9']
+        python-version: ['3.7', '3.10']
         webserver: ['uwsgi']
         include:
-          - python-version: '3.9'
+          - python-version: '3.10'
             webserver: 'dev'
     defaults:
       run:

.github/workflows/lint.yaml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.6', '3.9']
+        python-version: ['3.7', '3.10']
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2

.github/workflows/osx_startup.yaml

@@ -29,8 +29,8 @@ jobs:
       id: pip-cache
       with:
         path: ~/Library/Caches/pip
-        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6
-        key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }}
+        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.7
+        key: pip-cache-3.7-${{ hashFiles('galaxy root/requirements.txt') }}
     - name: Cache tox env
       uses: actions/cache@v2
       with:

.github/workflows/reports_startup.yaml

@@ -0,0 +1,56 @@
+name: Reports startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+env:
+  YARN_INSTALL_OPTS: --frozen-lockfile
+concurrency:
+  group: reports-startup-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+
+  test:
+    name: Reports startup test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.10']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+    - 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: Cache tox env
+      uses: actions/cache@v2
+      with:
+        path: .tox
+        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
+    - uses: mvdbeek/gha-yarn-cache@master
+      with:
+        yarn-lock-file: 'galaxy root/client/yarn.lock'
+    - name: Install tox
+      run: pip install tox
+    - name: run tests
+      run: tox -e reports_startup
+      working-directory: 'galaxy root'

.github/workflows/test_galaxy_release.yaml

@@ -0,0 +1,25 @@
+name: Test Galaxy release script
+on:
+  push:
+    paths:
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+  pull_request:
+    paths:
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+concurrency:
+  group: test-galaxy-release-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Run tests
+        run: ./test/release.sh

.github/workflows/unit.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6', '3.9']
+        python-version: ['3.7', '3.10']
     steps:
       - uses: actions/checkout@v2
         with:
@@ -47,3 +47,8 @@ jobs:
       - name: Run tests
         run: tox -e unit
         working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Unit test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_unit_tests.html'

Makefile

@@ -4,6 +4,7 @@ VENV?=.venv
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
 RELEASE_CURR:=22.01
 RELEASE_UPSTREAM:=upstream
+TARGET_BRANCH=$(RELEASE_UPSTREAM)/dev
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
 DOCS_DIR=doc
@@ -37,6 +38,9 @@ docs-develop: ## Fast doc generation and more warnings (for development)
 setup-venv:
 	if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
 
+diff-format:
+	$(IN_VENV) darker -r $(TARGET_BRANCH)
+
 list-dependency-updates: setup-venv
 	$(IN_VENV) pip list --outdated --format=columns
 
@@ -141,7 +145,7 @@ $(CWL_TARGETS):
 
 generate-cwl-conformance-tests: $(CWL_TARGETS)  ## Initialise CWL conformance tests
 
-clean-cwl-conformance-tests:  # Clean CWL conformance tests
+clean-cwl-conformance-tests:  ## Clean CWL conformance tests
 	for f in $(CWL_TARGETS); do \
 		if [ $$(basename "$$f") = conformance_tests.yaml ]; then \
 			rm -rf $$(dirname "$$f"); \

client/src/bundleEntries.js

@@ -17,7 +17,6 @@ export { TracksterUI } from "viz/trackster";
 import Circster from "viz/circster";
 export { PhylovizView as phyloviz } from "viz/phyloviz";
 export { SweepsterVisualization, SweepsterVisualizationView } from "viz/sweepster";
-import GalaxyLibrary from "galaxy.library";
 export { createTabularDatasetChunkedView } from "mvc/dataset/data";
 import { HistoryCollection } from "mvc/history/history-model";
 export { History } from "mvc/history/history-model";
@@ -44,10 +43,6 @@ export function circster(options) {
     new Circster.GalaxyApp(options);
 }
 
-export function library(options) {
-    new GalaxyLibrary.GalaxyApp(options);
-}
-
 export function multiHistory(options) {
     const histories = new HistoryCollection([], {
         includeDeleted: options.includingDeleted,

client/src/components/CopyToClipboard.vue

@@ -1,5 +1,5 @@
 <template>
-    <font-awesome-icon :title="title" :icon="['far', 'copy']" @click="copy(text, message)" />
+    <font-awesome-icon class="cursor-pointer" :title="title" :icon="['far', 'copy']" @click="copy(text, message)" />
 </template>
 
 <script>

client/src/components/DatasetInformation/DatasetAttributes.test.js

@@ -9,7 +9,7 @@ import flushPromises from "flush-promises";
 
 const localVue = getLocalVue();
 
-jest.mock("components/History/caching");
+jest.mock("components/providers/History/caching");
 
 function buildWrapper(conversion_disable = false) {
     return mount(DatasetAttributes, {

client/src/components/DatasetInformation/DatasetInformation.test.js

@@ -7,7 +7,7 @@ import datasetResponse from "./testData/datasetResponse";
 import flushPromises from "flush-promises";
 import moment from "moment";
 
-jest.mock("components/History/caching");
+jest.mock("components/providers/History/caching");
 const HDA_ID = "FOO_HDA_ID";
 
 const mockDatasetProvider = {

client/src/components/FilesDialog/FilesDialog.test.js

@@ -9,6 +9,7 @@ import axios from "axios";
 import BootstrapVue from "bootstrap-vue";
 
 import {
+    ftpId,
     rootId,
     directoryId,
     subDirectoryId,
@@ -19,6 +20,7 @@ import {
     directory2RecursiveResponse,
     directory1Response,
     subsubdirectoryResponse,
+    someErrorText,
 } from "./testingData";
 import { selectionStates } from "components/SelectionDialog/selectionStates";
 
@@ -44,6 +46,11 @@ const initComponent = async (props) => {
         axiosMock.onGet(path).reply(200, response);
     }
 
+    axiosMock.onGet("/api/remote_files?target=gxfiles://empty-dir").reply(404, {
+        err_msg: someErrorText,
+        err_code: 404,
+    });
+
     const wrapper = shallowMount(FilesDialog, {
         localVue,
         propsData: props,
@@ -193,6 +200,43 @@ describe("FilesDialog, file mode", () => {
         const rootNode = utils.getRenderedDirectory(rootId);
         expect(rootNode._rowVariant).toBe(selectionStates.selected);
     });
+
+    it("should show ftp helper only in ftp directory", async () => {
+        // open some other directory than ftp
+        await utils.open_root_folder();
+        // check that ftp helper is not visible
+        expect(wrapper.vm.showFTPHelper).toBe(false);
+        expect(wrapper.find("#helper").exists()).toBe(false);
+        // back to root folder
+        await utils.navigateBack();
+
+        // open ftp directory
+        await utils.openDirectory(ftpId);
+        // check that ftp helper is visible
+        expect(wrapper.vm.showFTPHelper).toBe(true);
+        expect(wrapper.find("#helper").exists()).toBe(true);
+    });
+
+    it("should show loading error and can return back", async () => {
+        expect(wrapper.vm.errorMessage).toBeNull();
+
+        // open directory with error
+        await utils.openDirectory("empty-dir");
+        // assert that error message is set and showed
+        expect(wrapper.vm.errorMessage).toBe(someErrorText);
+        expect(wrapper.html()).toContain(someErrorText);
+
+        // assert that OK button is disabled
+        expect(wrapper.vm.hasValue).toBe(false);
+
+        // back to the root folder
+        await wrapper.find("#back-btn").trigger("click");
+        await flushPromises();
+        expect(wrapper.vm.items.length).toBe(rootResponse.length);
+
+        // assert that OK button is disabled
+        expect(wrapper.vm.hasValue).toBe(false);
+    });
 });
 
 describe("FilesDialog, directory mode", () => {
@@ -238,6 +282,27 @@ describe("FilesDialog, directory mode", () => {
         //should close modal
         expect(wrapper.vm.modalShow).toBe(false);
     });
+
+    it("should show loading error and can return back", async () => {
+        expect(wrapper.vm.errorMessage).toBeNull();
+
+        // open directory with error
+        await utils.openDirectory("empty-dir");
+        // assert that error message is set and showed
+        expect(wrapper.vm.errorMessage).toBe(someErrorText);
+        expect(wrapper.html()).toContain(someErrorText);
+
+        // assert that OK button is disabled
+        expect(wrapper.vm.hasValue).toBe(false);
+
+        // back to the root folder
+        await wrapper.find("#back-btn").trigger("click");
+        await flushPromises();
+        expect(wrapper.vm.items.length).toBe(rootResponse.length);
+
+        // assert that OK button is disabled
+        expect(wrapper.vm.hasValue).toBe(false);
+    });
 });
 
 /** Util methods **/