diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml new file mode 100644 index 00000000000..a8cd3f3f7a4 --- /dev/null +++ b/.github/workflows/converter_tests.yaml @@ -0,0 +1,29 @@ +name: Converter tests +on: [push, pull_request] +jobs: + + test: + name: Test + runs-on: ubuntu-18.04 + strategy: + matrix: + python-version: [3.7] + steps: + - uses: actions/checkout@v1 + with: + fetch-depth: 1 + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Cache venv dir + uses: actions/cache@v1 + id: pip-cache + with: + path: ~/.cache/pip + key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }} + - name: fetch test data + run: git clone https://github.com/galaxyproject/galaxy-test-data && cp -R galaxy-test-data/* test-data + - name: Install planemo + run: pip install planemo + - name: Run tests + run: 'planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root . lib/galaxy/datatypes/converters/*xml' diff --git a/client/styleguide.config.js b/client/styleguide.config.js index d3d7d64d7e9..511dc134efc 100644 --- a/client/styleguide.config.js +++ b/client/styleguide.config.js @@ -2,8 +2,9 @@ const path = require("path"); const glob = require("glob"); const fs = require("fs"); const merge = require("webpack-merge"); +const baseConfig = require("./webpack.config.js") -let webpackConfig = require("./webpack.config.js"); +const webpackConfig = baseConfig(); const fileLoaderTest = /\.(png|jpg|jpeg|gif|svg|woff|woff2|ttf|eot)(\?.*$|$)/; @@ -37,9 +38,9 @@ const fileLoaderConfigRule = { rules: [{ test: fileLoaderTest, use: ["file-loade webpackConfig.module = merge.smart(webpackConfig.module, fileLoaderConfigRule); webpackConfig.output.publicPath = ""; -webpackConfig.resolve.modules.push( path.join(__dirname, "galaxy/style/scss") ); +webpackConfig.resolve.modules.push(path.join(__dirname, "galaxy/style/scss")); -galaxyStyleDocs = [] +const galaxyStyleDocs = []; glob.sync("./galaxy/docs/galaxy-*.md").forEach(file => { const name = file.match(/galaxy-(\w+).md/)[1]; galaxyStyleDocs.push({ name: name, content: file }); @@ -47,26 +48,29 @@ glob.sync("./galaxy/docs/galaxy-*.md").forEach(file => { const sections = [ { - name: 'Components', - // Components that are directories will get their own section - sections: glob.sync("./galaxy/scripts/components/*").map(file => { - if (fs.lstatSync(file).isDirectory()) { - return { - name: path.basename(file), - components: file + "/**/*.vue" - }; - } - }).filter( v => v ), - // ...while top level components are handled here. - components: './galaxy/scripts/components/*.vue', + name: "Galaxy styles", + sections: galaxyStyleDocs }, { - name: 'Galaxy styles', - sections: galaxyStyleDocs + name: "Basic Bootstrap Styles", + content: "./galaxy/docs/bootstrap.md" }, { - name: "Basic Bootstrap Styles", - content: "./galaxy/docs/bootstrap.md" + name: "Components", + // Components that are directories will get their own section + sections: glob + .sync("./galaxy/scripts/components/*") + .map(file => { + if (fs.lstatSync(file).isDirectory()) { + return { + name: path.basename(file), + components: file + "/**/*.vue" + }; + } + }) + .filter(v => v), + // ...while top level components are handled here. + components: "./galaxy/scripts/components/*.vue" } ]; diff --git a/client/webpack.config.js b/client/webpack.config.js index 2c45fbb7499..4ea1b1e85c9 100644 --- a/client/webpack.config.js +++ b/client/webpack.config.js @@ -15,7 +15,7 @@ module.exports = (env = {}, argv = {}) => { // environment name based on -d, -p, webpack flag const targetEnv = argv.mode || "development"; - let buildconfig = { + const buildconfig = { entry: { login: ["polyfills", "bundleEntries", "entry/login"], analysis: ["polyfills", "bundleEntries", "entry/analysis"], diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index 9f5db55df75..f2aacad6d03 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -142,6 +142,7 @@ + diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml index 1587ff83cab..65ace10fc93 100644 --- a/lib/galaxy/datatypes/converters/bam_to_bai.xml +++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml @@ -1,14 +1,20 @@ - diff --git a/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml b/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml index faf09918f64..a7f5b48813f 100644 --- a/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml +++ b/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml @@ -12,6 +12,12 @@ bcftools view -o '$output1' -O b '$input1' + + + + + + diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml index cd64113d236..2b2d7ab6f53 100644 --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -38,6 +38,12 @@ + + + + + + diff --git a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml index 08d91cddf72..270b98bcf16 100644 --- a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml @@ -1,5 +1,9 @@ - diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml index 26a4eeb2f2d..79ed48a9ef6 100644 --- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml @@ -1,6 +1,9 @@ - + + + python + python '$__tool_directory__/bed_to_gff_converter.py' '$input1' '$output1' @@ -8,6 +11,12 @@ + + + + + + diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml index bb171c0cd0b..98618ef4c68 100644 --- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml @@ -1,5 +1,8 @@ - diff --git a/lib/galaxy/datatypes/converters/biom2_to_biom1.xml b/lib/galaxy/datatypes/converters/biom2_to_biom1.xml index 559763ff74f..a280bd84432 100644 --- a/lib/galaxy/datatypes/converters/biom2_to_biom1.xml +++ b/lib/galaxy/datatypes/converters/biom2_to_biom1.xml @@ -9,6 +9,16 @@ + + + + + + + + + + diff --git a/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml b/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml index 3d5ee318b78..ebe660218a0 100644 --- a/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml +++ b/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml @@ -1,4 +1,7 @@ -