sequenceserver 2.0.0 → 2.1.0
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- checksums.yaml +4 -4
- data/lib/sequenceserver/api_errors.rb +24 -2
- data/lib/sequenceserver/blast/job.rb +41 -7
- data/lib/sequenceserver/blast/report.rb +36 -30
- data/lib/sequenceserver/config.rb +49 -27
- data/lib/sequenceserver/job.rb +13 -3
- data/lib/sequenceserver/job_remover.rb +25 -29
- data/lib/sequenceserver/refinements.rb +15 -0
- data/lib/sequenceserver/routes.rb +69 -7
- data/lib/sequenceserver/sequence.rb +8 -7
- data/lib/sequenceserver/sys.rb +2 -2
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver/zip_file_generator.rb +56 -0
- data/lib/sequenceserver.rb +1 -0
- data/public/config.js +149 -143
- data/public/css/sequenceserver.css +44 -3
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/alignment_exporter.js +16 -8
- data/public/js/circos.js +370 -234
- data/public/js/cloud_share_modal.js +216 -0
- data/public/js/databases.js +144 -0
- data/public/js/databases_tree.js +42 -113
- data/public/js/dnd.js +164 -0
- data/public/js/error_modal.js +4 -11
- data/public/js/exporter.js +7 -3
- data/public/js/form.js +260 -0
- data/public/js/grapher.js +113 -106
- data/public/js/hit.js +80 -67
- data/public/js/hits_overview.js +2 -2
- data/public/js/hsp.js +343 -288
- data/public/js/jquery_world.js +4 -4
- data/public/js/mailto.js +36 -0
- data/public/js/options.js +84 -0
- data/public/js/query.js +319 -59
- data/public/js/report.js +315 -269
- data/public/js/report_root.js +75 -0
- data/public/js/search.js +28 -1011
- data/public/js/search_button.js +195 -0
- data/public/js/sequence.js +2409 -2411
- data/public/js/sequence_modal.js +152 -159
- data/public/js/share_url.js +23 -0
- data/public/js/sidebar.js +262 -83
- data/public/js/tests/database.spec.js +60 -0
- data/public/js/tests/mock_data/databases.json +91 -0
- data/public/js/tests/mock_data/long_response.json +269 -0
- data/public/js/tests/mock_data/short_response.json +2240 -0
- data/public/js/tests/report.spec.js +99 -0
- data/public/js/tests/search_button.spec.js +14 -0
- data/public/js/tests/search_query.spec.js +41 -0
- data/public/packages/circosJS@1.7.0.js +1640 -0
- data/public/packages/jquery-ui@1.11.4.js +16624 -0
- data/public/sequenceserver-report.min.js +2425 -19
- data/public/sequenceserver-search.min.js +2337 -15
- data/public/vendor/github/jspm/nodelibs-assert@0.1.0/index.js +2 -0
- data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-assert@0.1.0}/package.json +1 -1
- data/public/vendor/github/jspm/nodelibs-assert@0.1.0.js +1 -0
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.1/package.json +6 -0
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.1.js +1 -0
- data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/package.json +2 -2
- data/public/vendor/github/jspm/nodelibs-process@0.1.2.js +1 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js +2 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json +6 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0.js +1 -0
- data/public/vendor/npm/assert@1.5.0/CHANGELOG.md +8 -0
- data/public/vendor/npm/assert@1.5.0/README.md +105 -0
- data/public/vendor/npm/assert@1.5.0/assert.js +327 -0
- data/public/vendor/npm/assert@1.5.0/package.json +32 -0
- data/public/vendor/npm/assert@1.5.0/test.js +288 -0
- data/public/vendor/npm/assert@1.5.0.js +1 -0
- data/public/vendor/npm/{base64-js@0.0.8/LICENSE.MIT → base64-js@1.5.1/LICENSE} +1 -1
- data/public/vendor/npm/{base64-js@0.0.8 → base64-js@1.5.1}/README.md +10 -7
- data/public/vendor/npm/base64-js@1.5.1/base64js.min.js +3 -0
- data/public/vendor/npm/base64-js@1.5.1/index.d.ts +3 -0
- data/public/vendor/npm/base64-js@1.5.1/index.js +151 -0
- data/public/vendor/npm/base64-js@1.5.1/package.json +47 -0
- data/public/vendor/npm/base64-js@1.5.1.js +1 -0
- data/public/vendor/npm/buffer@5.7.1/AUTHORS.md +70 -0
- data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/README.md +111 -41
- data/public/vendor/npm/buffer@5.7.1/index.d.ts +186 -0
- data/public/vendor/npm/buffer@5.7.1/index.js +1817 -0
- data/public/vendor/npm/buffer@5.7.1/package.json +96 -0
- data/public/vendor/npm/buffer@5.7.1.js +1 -0
- data/public/vendor/npm/core-util-is@1.0.3/LICENSE +19 -0
- data/public/vendor/npm/core-util-is@1.0.3/lib/util.js +64 -0
- data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/package.json +13 -1
- data/public/vendor/npm/core-util-is@1.0.3.js +1 -0
- data/public/vendor/npm/events@1.0.2/tests/add-listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/check-listener-leaks.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/common.js +1 -1
- data/public/vendor/npm/events@1.0.2/tests/index.js +13 -13
- data/public/vendor/npm/events@1.0.2/tests/listeners-side-effects.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/max-listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/modify-in-emit.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/num-args.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/once.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/remove-all-listeners.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/remove-listeners.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/set-max-listeners-side-effects.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/subclass.js +3 -3
- data/public/vendor/npm/events@1.0.2.js +1 -1
- data/public/vendor/npm/ieee754@1.2.1/LICENSE +11 -0
- data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/README.md +12 -8
- data/public/vendor/npm/ieee754@1.2.1/index.d.ts +10 -0
- data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/index.js +6 -6
- data/public/vendor/npm/ieee754@1.2.1/package.json +52 -0
- data/public/vendor/npm/ieee754@1.2.1.js +1 -0
- data/public/vendor/npm/{is-array@1.0.1 → indexof@0.0.1}/Makefile +3 -3
- data/public/vendor/npm/indexof@0.0.1/Readme.md +15 -0
- data/public/vendor/npm/indexof@0.0.1/component.json +10 -0
- data/public/vendor/npm/indexof@0.0.1/index.js +11 -0
- data/public/vendor/npm/indexof@0.0.1/package.json +12 -0
- data/public/vendor/npm/indexof@0.0.1.js +1 -0
- data/public/vendor/npm/inherits@2.0.1/inherits.js +1 -1
- data/public/vendor/npm/inherits@2.0.1.js +1 -1
- data/public/vendor/npm/isarray@0.0.1.js +1 -1
- data/public/vendor/npm/js-tokens@4.0.0/index.js +23 -0
- data/public/vendor/npm/js-tokens@4.0.0/package.json +30 -0
- data/public/vendor/npm/js-tokens@4.0.0.js +1 -0
- data/public/vendor/npm/loose-envify@1.4.0/LICENSE +21 -0
- data/public/vendor/npm/loose-envify@1.4.0/README.md +45 -0
- data/public/vendor/npm/loose-envify@1.4.0/cli.js +12 -0
- data/public/vendor/npm/loose-envify@1.4.0/custom.js +3 -0
- data/public/vendor/npm/loose-envify@1.4.0/index.js +5 -0
- data/public/vendor/npm/loose-envify@1.4.0/loose-envify.js +33 -0
- data/public/vendor/npm/loose-envify@1.4.0/package.json +36 -0
- data/public/vendor/npm/loose-envify@1.4.0/replace.js +52 -0
- data/public/vendor/npm/loose-envify@1.4.0.js +1 -0
- data/public/vendor/npm/object-assign@4.1.1/index.js +90 -0
- data/public/vendor/npm/object-assign@4.1.1/package.json +42 -0
- data/public/vendor/npm/object-assign@4.1.1.js +1 -0
- data/public/vendor/npm/path-browserify@0.0.0/index.js +1 -1
- data/public/vendor/npm/path-browserify@0.0.0.js +1 -1
- data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/README.md +4 -1
- data/public/vendor/npm/process@0.11.10/browser.js +184 -0
- data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/package.json +10 -1
- data/public/vendor/npm/process@0.11.10/test.js +185 -0
- data/public/vendor/npm/process@0.11.10.js +1 -0
- data/public/vendor/npm/react-dom@18.0.0/LICENSE +21 -0
- data/public/vendor/npm/react-dom@18.0.0/README.md +50 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.development.js +4771 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.production.min.js +85 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.development.js +4813 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.production.min.js +1705 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.development.js +4746 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.production.min.js +90 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.development.js +4714 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.production.min.js +1746 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.development.js +1017 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.production.min.js +617 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.development.js +20092 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.production.min.js +322 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.profiling.min.js +364 -0
- data/public/vendor/npm/react-dom@18.0.0/client.js +27 -0
- data/public/vendor/npm/react-dom@18.0.0/index.js +23 -0
- data/public/vendor/npm/react-dom@18.0.0/package.json +62 -0
- data/public/vendor/npm/react-dom@18.0.0/profiling.js +23 -0
- data/public/vendor/npm/react-dom@18.0.0/server.browser.js +19 -0
- data/public/vendor/npm/react-dom@18.0.0/server.js +3 -0
- data/public/vendor/npm/react-dom@18.0.0/server.node.js +19 -0
- data/public/vendor/npm/react-dom@18.0.0/test-utils.js +9 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.development.js +4770 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.production.min.js +72 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.development.js +4745 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.production.min.js +74 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.development.js +1013 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.production.min.js +625 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.development.js +20106 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.production.min.js +269 -0
- data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.profiling.min.js +285 -0
- data/public/vendor/npm/react-dom@18.0.0.js +1 -0
- data/public/vendor/npm/react@18.0.0/LICENSE +21 -0
- data/public/vendor/npm/react@18.0.0/README.md +13 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.development.js +837 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.production.min.js +10 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.profiling.min.js +10 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.development.js +849 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.production.min.js +38 -0
- data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.profiling.min.js +38 -0
- data/public/vendor/npm/react@18.0.0/cjs/react.development.js +1746 -0
- data/public/vendor/npm/react@18.0.0/cjs/react.production.min.js +26 -0
- data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.development.js +10 -0
- data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.production.min.js +12 -0
- data/public/vendor/npm/react@18.0.0/index.js +9 -0
- data/public/vendor/npm/react@18.0.0/jsx-dev-runtime.js +9 -0
- data/public/vendor/npm/react@18.0.0/jsx-runtime.js +9 -0
- data/public/vendor/npm/react@18.0.0/package.json +47 -0
- data/public/vendor/npm/react@18.0.0/react.shared-subset.js +9 -0
- data/public/vendor/npm/react@18.0.0/umd/react.development.js +2186 -0
- data/public/vendor/npm/react@18.0.0/umd/react.production.min.js +33 -0
- data/public/vendor/npm/react@18.0.0/umd/react.profiling.min.js +33 -0
- data/public/vendor/npm/react@18.0.0.js +1 -0
- data/public/vendor/npm/readable-stream@1.1.14/LICENSE +18 -0
- data/public/vendor/npm/readable-stream@1.1.14/duplex.js +2 -0
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_duplex.js +5 -5
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_passthrough.js +3 -3
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_readable.js +10 -10
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_transform.js +4 -4
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_writable.js +6 -6
- data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/package.json +1 -1
- data/public/vendor/npm/readable-stream@1.1.14/passthrough.js +2 -0
- data/public/vendor/npm/readable-stream@1.1.14/readable.js +13 -0
- data/public/vendor/npm/readable-stream@1.1.14/transform.js +2 -0
- data/public/vendor/npm/readable-stream@1.1.14/writable.js +2 -0
- data/public/vendor/npm/readable-stream@1.1.14.js +1 -0
- data/public/vendor/npm/scheduler@0.21.0/LICENSE +21 -0
- data/public/vendor/npm/scheduler@0.21.0/README.md +9 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.development.js +530 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.production.min.js +20 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.development.js +153 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.production.min.js +14 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.development.js +444 -0
- data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.production.min.js +19 -0
- data/public/vendor/npm/scheduler@0.21.0/index.js +9 -0
- data/public/vendor/npm/scheduler@0.21.0/package.json +36 -0
- data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.development.js +701 -0
- data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.production.min.js +21 -0
- data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.development.js +154 -0
- data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.production.min.js +148 -0
- data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.profiling.min.js +148 -0
- data/public/vendor/npm/scheduler@0.21.0/unstable_mock.js +9 -0
- data/public/vendor/npm/scheduler@0.21.0/unstable_post_task.js +9 -0
- data/public/vendor/npm/scheduler@0.21.0.js +1 -0
- data/public/vendor/npm/stream-browserify@1.0.0/index.js +7 -7
- data/public/vendor/npm/stream-browserify@1.0.0/test/buf.js +5 -5
- data/public/vendor/npm/stream-browserify@1.0.0.js +1 -1
- data/public/vendor/npm/string_decoder@0.10.31/index.js +2 -2
- data/public/vendor/npm/string_decoder@0.10.31.js +1 -1
- data/public/vendor/npm/util@0.10.3/support/isBuffer.js +1 -1
- data/public/vendor/npm/util@0.10.3/test/browser/inspect.js +2 -2
- data/public/vendor/npm/util@0.10.3/test/browser/is.js +3 -3
- data/public/vendor/npm/util@0.10.3/test/node/debug.js +4 -4
- data/public/vendor/npm/util@0.10.3/test/node/format.js +2 -2
- data/public/vendor/npm/util@0.10.3/test/node/inspect.js +3 -3
- data/public/vendor/npm/util@0.10.3/test/node/log.js +3 -3
- data/public/vendor/npm/util@0.10.3/test/node/util.js +3 -3
- data/public/vendor/npm/util@0.10.3/util.js +3 -3
- data/public/vendor/npm/util@0.10.3.js +1 -1
- data/public/vendor/npm/vm-browserify@0.0.4/LICENSE +18 -0
- data/public/vendor/npm/vm-browserify@0.0.4/example/run/bundle.js +376 -0
- data/public/vendor/npm/vm-browserify@0.0.4/example/run/entry.js +6 -0
- data/public/vendor/npm/vm-browserify@0.0.4/example/run/index.html +9 -0
- data/public/vendor/npm/vm-browserify@0.0.4/example/run/server.js +6 -0
- data/public/vendor/npm/vm-browserify@0.0.4/index.js +139 -0
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- data/public/vendor/npm/vm-browserify@0.0.4/readme.markdown +67 -0
- data/public/vendor/npm/vm-browserify@0.0.4/test/vm.js +34 -0
- data/public/vendor/npm/vm-browserify@0.0.4.js +1 -0
- data/public/vendor/npm/webshim@1.15.8/Gruntfile.js +4 -4
- data/public/vendor/npm/webshim@1.15.8/build/combobuild.js +2 -2
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/color-picker.js +1 -1
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- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/es6.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/excanvas.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/form-number-date-ui.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/moxie/js/moxie-html4.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/moxie/js/moxie-swf.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/sizzle.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/js-webshim/minified/shims/es6.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/src/shims/color-picker.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/src/shims/combos/10.js +1 -1
- data/public/vendor/npm/webshim@1.15.8/src/shims/combos/11.js +1 -1
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dest: 'dist/source-map.min.js'
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});
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}
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function buildFirefox() {
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console.log('\nCreating dist/SourceMap.jsm');
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var project = copy.createCommonJsProject({roots: [path.join(__dirname, 'lib')]});
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copy({
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40
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source: ['build/prefix-source-map.jsm', {
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project: project,
|
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require: ['source-map/source-map-consumer', 'source-map/source-map-generator', 'source-map/source-node']
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}, 'build/suffix-source-map.jsm'],
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|
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filter: [copy.filter.moduleDefines, removeAmdefine, makeNonRelative],
|
45
|
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dest: 'dist/SourceMap.jsm'
|
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});
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-
console.log('\nCreating dist/test/Utils.jsm');
|
48
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project = copy.createCommonJsProject({roots: [__dirname, path.join(__dirname, 'lib')]});
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copy({
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source: ['build/prefix-utils.jsm', 'build/assert-shim.js', {
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project: project,
|
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require: ['test/source-map/util']
|
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|
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}, 'build/suffix-utils.jsm'],
|
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|
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filter: [copy.filter.moduleDefines, removeAmdefine, makeNonRelative],
|
55
|
-
dest: 'dist/test/Utils.jsm'
|
56
|
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});
|
57
|
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function isTestFile(f) {
|
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|
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return /^test\-.*?\.js/.test(f);
|
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|
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}
|
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|
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var testFiles = fs.readdirSync(path.join(__dirname, 'test', 'source-map')).filter(isTestFile);
|
61
|
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testFiles.forEach(function(testFile) {
|
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console.log('\nCreating', path.join('dist', 'test', testFile.replace(/\-/g, '_')));
|
63
|
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copy({
|
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|
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source: ['build/test-prefix.js', path.join('test', 'source-map', testFile), 'build/test-suffix.js'],
|
65
|
-
filter: [removeAmdefine, makeNonRelative, function(input, source) {
|
66
|
-
return input.replace('define(', 'define("' + path.join('test', 'source-map', testFile.replace(/\.js$/, '')) + '", ["require", "exports", "module"], ');
|
67
|
-
}, function(input, source) {
|
68
|
-
return input.replace('{THIS_MODULE}', function() {
|
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|
-
return "test/source-map/" + testFile.replace(/\.js$/, '');
|
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|
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});
|
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|
-
}],
|
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|
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dest: path.join('dist', 'test', testFile.replace(/\-/g, '_'))
|
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|
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});
|
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|
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});
|
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|
-
}
|
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|
-
function ensureDir(name) {
|
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|
-
var dirExists = false;
|
78
|
-
try {
|
79
|
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dirExists = fs.statSync(name).isDirectory();
|
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|
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} catch (err) {}
|
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|
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if (!dirExists) {
|
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|
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fs.mkdirSync(name, 0777);
|
83
|
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}
|
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|
-
}
|
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|
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ensureDir("dist");
|
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|
-
ensureDir("dist/test");
|
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|
-
buildFirefox();
|
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|
-
buildBrowser();
|
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|
-
buildBrowserMin();
|
@@ -1,434 +0,0 @@
|
|
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|
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# Source Map
|
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|
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|
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This is a library to generate and consume the source map format
|
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|
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[described here][format].
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|
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This library is written in the Asynchronous Module Definition format, and works
|
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|
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in the following environments:
|
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|
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* Modern Browsers supporting ECMAScript 5 (either after the build, or with an
|
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AMD loader such as RequireJS)
|
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|
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* Inside Firefox (as a JSM file, after the build)
|
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* With NodeJS versions 0.8.X and higher
|
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## Node
|
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|
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$ npm install source-map
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|
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## Building from Source (for everywhere else)
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|
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|
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Install Node and then run
|
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|
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$ git clone https://fitzgen@github.com/mozilla/source-map.git
|
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$ cd source-map
|
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$ npm link .
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|
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Next, run
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|
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$ node Makefile.dryice.js
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|
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|
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This should spew a bunch of stuff to stdout, and create the following files:
|
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|
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* `dist/source-map.js` - The unminified browser version.
|
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|
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* `dist/source-map.min.js` - The minified browser version.
|
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|
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* `dist/SourceMap.jsm` - The JavaScript Module for inclusion in Firefox source.
|
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|
40
|
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## Examples
|
41
|
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|
42
|
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### Consuming a source map
|
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|
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|
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|
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var rawSourceMap = {
|
45
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version: 3,
|
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file: 'min.js',
|
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names: ['bar', 'baz', 'n'],
|
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sources: ['one.js', 'two.js'],
|
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|
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sourceRoot: 'http://example.com/www/js/',
|
50
|
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mappings: 'CAAC,IAAI,IAAM,SAAUA,GAClB,OAAOC,IAAID;CCDb,IAAI,IAAM,SAAUE,GAClB,OAAOA'
|
51
|
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};
|
52
|
-
|
53
|
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var smc = new SourceMapConsumer(rawSourceMap);
|
54
|
-
|
55
|
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console.log(smc.sources);
|
56
|
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// [ 'http://example.com/www/js/one.js',
|
57
|
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// 'http://example.com/www/js/two.js' ]
|
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|
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|
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|
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console.log(smc.originalPositionFor({
|
60
|
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line: 2,
|
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|
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column: 28
|
62
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}));
|
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|
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// { source: 'http://example.com/www/js/two.js',
|
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// line: 2,
|
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|
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// column: 10,
|
66
|
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// name: 'n' }
|
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|
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|
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|
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console.log(smc.generatedPositionFor({
|
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|
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source: 'http://example.com/www/js/two.js',
|
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line: 2,
|
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|
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column: 10
|
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|
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}));
|
73
|
-
// { line: 2, column: 28 }
|
74
|
-
|
75
|
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smc.eachMapping(function (m) {
|
76
|
-
// ...
|
77
|
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});
|
78
|
-
|
79
|
-
### Generating a source map
|
80
|
-
|
81
|
-
In depth guide:
|
82
|
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[**Compiling to JavaScript, and Debugging with Source Maps**](https://hacks.mozilla.org/2013/05/compiling-to-javascript-and-debugging-with-source-maps/)
|
83
|
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|
84
|
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#### With SourceNode (high level API)
|
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|
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|
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|
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function compile(ast) {
|
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|
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switch (ast.type) {
|
88
|
-
case 'BinaryExpression':
|
89
|
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return new SourceNode(
|
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|
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ast.location.line,
|
91
|
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ast.location.column,
|
92
|
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ast.location.source,
|
93
|
-
[compile(ast.left), " + ", compile(ast.right)]
|
94
|
-
);
|
95
|
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case 'Literal':
|
96
|
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return new SourceNode(
|
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|
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ast.location.line,
|
98
|
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ast.location.column,
|
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|
-
ast.location.source,
|
100
|
-
String(ast.value)
|
101
|
-
);
|
102
|
-
// ...
|
103
|
-
default:
|
104
|
-
throw new Error("Bad AST");
|
105
|
-
}
|
106
|
-
}
|
107
|
-
|
108
|
-
var ast = parse("40 + 2", "add.js");
|
109
|
-
console.log(compile(ast).toStringWithSourceMap({
|
110
|
-
file: 'add.js'
|
111
|
-
}));
|
112
|
-
// { code: '40 + 2',
|
113
|
-
// map: [object SourceMapGenerator] }
|
114
|
-
|
115
|
-
#### With SourceMapGenerator (low level API)
|
116
|
-
|
117
|
-
var map = new SourceMapGenerator({
|
118
|
-
file: "source-mapped.js"
|
119
|
-
});
|
120
|
-
|
121
|
-
map.addMapping({
|
122
|
-
generated: {
|
123
|
-
line: 10,
|
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|
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column: 35
|
125
|
-
},
|
126
|
-
source: "foo.js",
|
127
|
-
original: {
|
128
|
-
line: 33,
|
129
|
-
column: 2
|
130
|
-
},
|
131
|
-
name: "christopher"
|
132
|
-
});
|
133
|
-
|
134
|
-
console.log(map.toString());
|
135
|
-
// '{"version":3,"file":"source-mapped.js","sources":["foo.js"],"names":["christopher"],"mappings":";;;;;;;;;mCAgCEA"}'
|
136
|
-
|
137
|
-
## API
|
138
|
-
|
139
|
-
Get a reference to the module:
|
140
|
-
|
141
|
-
// NodeJS
|
142
|
-
var sourceMap = require('source-map');
|
143
|
-
|
144
|
-
// Browser builds
|
145
|
-
var sourceMap = window.sourceMap;
|
146
|
-
|
147
|
-
// Inside Firefox
|
148
|
-
let sourceMap = {};
|
149
|
-
Components.utils.import('resource:///modules/devtools/SourceMap.jsm', sourceMap);
|
150
|
-
|
151
|
-
### SourceMapConsumer
|
152
|
-
|
153
|
-
A SourceMapConsumer instance represents a parsed source map which we can query
|
154
|
-
for information about the original file positions by giving it a file position
|
155
|
-
in the generated source.
|
156
|
-
|
157
|
-
#### new SourceMapConsumer(rawSourceMap)
|
158
|
-
|
159
|
-
The only parameter is the raw source map (either as a string which can be
|
160
|
-
`JSON.parse`'d, or an object). According to the spec, source maps have the
|
161
|
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following attributes:
|
162
|
-
|
163
|
-
* `version`: Which version of the source map spec this map is following.
|
164
|
-
|
165
|
-
* `sources`: An array of URLs to the original source files.
|
166
|
-
|
167
|
-
* `names`: An array of identifiers which can be referrenced by individual
|
168
|
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mappings.
|
169
|
-
|
170
|
-
* `sourceRoot`: Optional. The URL root from which all sources are relative.
|
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|
-
|
172
|
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* `sourcesContent`: Optional. An array of contents of the original source files.
|
173
|
-
|
174
|
-
* `mappings`: A string of base64 VLQs which contain the actual mappings.
|
175
|
-
|
176
|
-
* `file`: The generated filename this source map is associated with.
|
177
|
-
|
178
|
-
#### SourceMapConsumer.prototype.originalPositionFor(generatedPosition)
|
179
|
-
|
180
|
-
Returns the original source, line, and column information for the generated
|
181
|
-
source's line and column positions provided. The only argument is an object with
|
182
|
-
the following properties:
|
183
|
-
|
184
|
-
* `line`: The line number in the generated source.
|
185
|
-
|
186
|
-
* `column`: The column number in the generated source.
|
187
|
-
|
188
|
-
and an object is returned with the following properties:
|
189
|
-
|
190
|
-
* `source`: The original source file, or null if this information is not
|
191
|
-
available.
|
192
|
-
|
193
|
-
* `line`: The line number in the original source, or null if this information is
|
194
|
-
not available.
|
195
|
-
|
196
|
-
* `column`: The column number in the original source, or null or null if this
|
197
|
-
information is not available.
|
198
|
-
|
199
|
-
* `name`: The original identifier, or null if this information is not available.
|
200
|
-
|
201
|
-
#### SourceMapConsumer.prototype.generatedPositionFor(originalPosition)
|
202
|
-
|
203
|
-
Returns the generated line and column information for the original source,
|
204
|
-
line, and column positions provided. The only argument is an object with
|
205
|
-
the following properties:
|
206
|
-
|
207
|
-
* `source`: The filename of the original source.
|
208
|
-
|
209
|
-
* `line`: The line number in the original source.
|
210
|
-
|
211
|
-
* `column`: The column number in the original source.
|
212
|
-
|
213
|
-
and an object is returned with the following properties:
|
214
|
-
|
215
|
-
* `line`: The line number in the generated source, or null.
|
216
|
-
|
217
|
-
* `column`: The column number in the generated source, or null.
|
218
|
-
|
219
|
-
#### SourceMapConsumer.prototype.sourceContentFor(source)
|
220
|
-
|
221
|
-
Returns the original source content for the source provided. The only
|
222
|
-
argument is the URL of the original source file.
|
223
|
-
|
224
|
-
#### SourceMapConsumer.prototype.eachMapping(callback, context, order)
|
225
|
-
|
226
|
-
Iterate over each mapping between an original source/line/column and a
|
227
|
-
generated line/column in this source map.
|
228
|
-
|
229
|
-
* `callback`: The function that is called with each mapping. Mappings have the
|
230
|
-
form `{ source, generatedLine, generatedColumn, originalLine, originalColumn,
|
231
|
-
name }`
|
232
|
-
|
233
|
-
* `context`: Optional. If specified, this object will be the value of `this`
|
234
|
-
every time that `callback` is called.
|
235
|
-
|
236
|
-
* `order`: Either `SourceMapConsumer.GENERATED_ORDER` or
|
237
|
-
`SourceMapConsumer.ORIGINAL_ORDER`. Specifies whether you want to iterate over
|
238
|
-
the mappings sorted by the generated file's line/column order or the
|
239
|
-
original's source/line/column order, respectively. Defaults to
|
240
|
-
`SourceMapConsumer.GENERATED_ORDER`.
|
241
|
-
|
242
|
-
### SourceMapGenerator
|
243
|
-
|
244
|
-
An instance of the SourceMapGenerator represents a source map which is being
|
245
|
-
built incrementally.
|
246
|
-
|
247
|
-
#### new SourceMapGenerator(startOfSourceMap)
|
248
|
-
|
249
|
-
To create a new one, you must pass an object with the following properties:
|
250
|
-
|
251
|
-
* `file`: The filename of the generated source that this source map is
|
252
|
-
associated with.
|
253
|
-
|
254
|
-
* `sourceRoot`: An optional root for all relative URLs in this source map.
|
255
|
-
|
256
|
-
#### SourceMapGenerator.fromSourceMap(sourceMapConsumer)
|
257
|
-
|
258
|
-
Creates a new SourceMapGenerator based on a SourceMapConsumer
|
259
|
-
|
260
|
-
* `sourceMapConsumer` The SourceMap.
|
261
|
-
|
262
|
-
#### SourceMapGenerator.prototype.addMapping(mapping)
|
263
|
-
|
264
|
-
Add a single mapping from original source line and column to the generated
|
265
|
-
source's line and column for this source map being created. The mapping object
|
266
|
-
should have the following properties:
|
267
|
-
|
268
|
-
* `generated`: An object with the generated line and column positions.
|
269
|
-
|
270
|
-
* `original`: An object with the original line and column positions.
|
271
|
-
|
272
|
-
* `source`: The original source file (relative to the sourceRoot).
|
273
|
-
|
274
|
-
* `name`: An optional original token name for this mapping.
|
275
|
-
|
276
|
-
#### SourceMapGenerator.prototype.setSourceContent(sourceFile, sourceContent)
|
277
|
-
|
278
|
-
Set the source content for an original source file.
|
279
|
-
|
280
|
-
* `sourceFile` the URL of the original source file.
|
281
|
-
|
282
|
-
* `sourceContent` the content of the source file.
|
283
|
-
|
284
|
-
#### SourceMapGenerator.prototype.applySourceMap(sourceMapConsumer[, sourceFile])
|
285
|
-
|
286
|
-
Applies a SourceMap for a source file to the SourceMap.
|
287
|
-
Each mapping to the supplied source file is rewritten using the
|
288
|
-
supplied SourceMap. Note: The resolution for the resulting mappings
|
289
|
-
is the minimium of this map and the supplied map.
|
290
|
-
|
291
|
-
* `sourceMapConsumer`: The SourceMap to be applied.
|
292
|
-
|
293
|
-
* `sourceFile`: Optional. The filename of the source file.
|
294
|
-
If omitted, sourceMapConsumer.file will be used.
|
295
|
-
|
296
|
-
#### SourceMapGenerator.prototype.toString()
|
297
|
-
|
298
|
-
Renders the source map being generated to a string.
|
299
|
-
|
300
|
-
### SourceNode
|
301
|
-
|
302
|
-
SourceNodes provide a way to abstract over interpolating and/or concatenating
|
303
|
-
snippets of generated JavaScript source code, while maintaining the line and
|
304
|
-
column information associated between those snippets and the original source
|
305
|
-
code. This is useful as the final intermediate representation a compiler might
|
306
|
-
use before outputting the generated JS and source map.
|
307
|
-
|
308
|
-
#### new SourceNode(line, column, source[, chunk[, name]])
|
309
|
-
|
310
|
-
* `line`: The original line number associated with this source node, or null if
|
311
|
-
it isn't associated with an original line.
|
312
|
-
|
313
|
-
* `column`: The original column number associated with this source node, or null
|
314
|
-
if it isn't associated with an original column.
|
315
|
-
|
316
|
-
* `source`: The original source's filename.
|
317
|
-
|
318
|
-
* `chunk`: Optional. Is immediately passed to `SourceNode.prototype.add`, see
|
319
|
-
below.
|
320
|
-
|
321
|
-
* `name`: Optional. The original identifier.
|
322
|
-
|
323
|
-
#### SourceNode.fromStringWithSourceMap(code, sourceMapConsumer)
|
324
|
-
|
325
|
-
Creates a SourceNode from generated code and a SourceMapConsumer.
|
326
|
-
|
327
|
-
* `code`: The generated code
|
328
|
-
|
329
|
-
* `sourceMapConsumer` The SourceMap for the generated code
|
330
|
-
|
331
|
-
#### SourceNode.prototype.add(chunk)
|
332
|
-
|
333
|
-
Add a chunk of generated JS to this source node.
|
334
|
-
|
335
|
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* `chunk`: A string snippet of generated JS code, another instance of
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`SourceNode`, or an array where each member is one of those things.
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#### SourceNode.prototype.prepend(chunk)
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Prepend a chunk of generated JS to this source node.
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* `chunk`: A string snippet of generated JS code, another instance of
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`SourceNode`, or an array where each member is one of those things.
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#### SourceNode.prototype.setSourceContent(sourceFile, sourceContent)
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Set the source content for a source file. This will be added to the
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`SourceMap` in the `sourcesContent` field.
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* `sourceFile`: The filename of the source file
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* `sourceContent`: The content of the source file
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#### SourceNode.prototype.walk(fn)
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Walk over the tree of JS snippets in this node and its children. The walking
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function is called once for each snippet of JS and is passed that snippet and
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the its original associated source's line/column location.
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* `fn`: The traversal function.
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#### SourceNode.prototype.walkSourceContents(fn)
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Walk over the tree of SourceNodes. The walking function is called for each
|
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source file content and is passed the filename and source content.
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* `fn`: The traversal function.
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#### SourceNode.prototype.join(sep)
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Like `Array.prototype.join` except for SourceNodes. Inserts the separator
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between each of this source node's children.
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* `sep`: The separator.
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#### SourceNode.prototype.replaceRight(pattern, replacement)
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Call `String.prototype.replace` on the very right-most source snippet. Useful
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for trimming whitespace from the end of a source node, etc.
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* `pattern`: The pattern to replace.
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* `replacement`: The thing to replace the pattern with.
|
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#### SourceNode.prototype.toString()
|
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|
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|
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Return the string representation of this source node. Walks over the tree and
|
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|
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concatenates all the various snippets together to one string.
|
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|
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### SourceNode.prototype.toStringWithSourceMap(startOfSourceMap)
|
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|
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|
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|
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Returns the string representation of this tree of source nodes, plus a
|
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SourceMapGenerator which contains all the mappings between the generated and
|
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original sources.
|
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|
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The arguments are the same as those to `new SourceMapGenerator`.
|
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|
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|
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## Tests
|
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|
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[![Build Status](https://travis-ci.org/mozilla/source-map.png?branch=master)](https://travis-ci.org/mozilla/source-map)
|
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|
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|
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Install NodeJS version 0.8.0 or greater, then run `node test/run-tests.js`.
|
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|
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|
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|
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To add new tests, create a new file named `test/test-<your new test name>.js`
|
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|
-
and export your test functions with names that start with "test", for example
|
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|
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|
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|
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exports["test doing the foo bar"] = function (assert, util) {
|
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|
-
...
|
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|
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};
|
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|
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|
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|
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The new test will be located automatically when you run the suite.
|
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|
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|
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|
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The `util` argument is the test utility module located at `test/source-map/util`.
|
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|
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|
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|
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The `assert` argument is a cut down version of node's assert module. You have
|
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|
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access to the following assertion functions:
|
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|
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|
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|
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* `doesNotThrow`
|
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|
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|
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|
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* `equal`
|
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|
-
|
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|
-
* `ok`
|
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|
-
|
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|
-
* `strictEqual`
|
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|
-
|
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|
-
* `throws`
|
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|
-
|
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|
-
(The reason for the restricted set of test functions is because we need the
|
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|
-
tests to run inside Firefox's test suite as well and so the assert module is
|
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|
-
shimmed in that environment. See `build/assert-shim.js`.)
|
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|
-
|
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|
-
[format]: https://docs.google.com/document/d/1U1RGAehQwRypUTovF1KRlpiOFze0b-_2gc6fAH0KY0k/edit
|
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|
-
[feature]: https://wiki.mozilla.org/DevTools/Features/SourceMap
|
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|
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[Dryice]: https://github.com/mozilla/dryice
|