diff --git a/.circleci/config.yml b/.circleci/config.yml index fbff0e753af..d128f4e46f1 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,7 +6,7 @@ defaults: &defaults working_directory: ~/repo docker: # specify the version you desire here - - image: circleci/node:8.9.4-browsers + - image: circleci/node:8.12.0-browsers version: 2 jobs: @@ -20,12 +20,7 @@ jobs: npm --version - checkout # Download and cache dependencies - - restore_cache: - keys: - - v1-dependencies-{{ checksum "package-lock.json" }} - # fallback to using the latest cache if no exact match is found - - v1-dependencies- - - run: npm install + - run: npm ci - run: name: "Ignore https to http switches on circleci in package lock (not sure why this happens)" command: "git diff --exit-code package-lock.json || sed -i 's/http:/https:/g' package-lock.json" @@ -96,7 +91,7 @@ jobs: command: | ./node_modules/http-server/bin/http-server --cors dist/ -p 3000 & \ cd end-to-end-tests && \ - npm install && \ + npm ci && \ ./node_modules/webdriver-manager/bin/webdriver-manager update --versions.chrome '2.37' && \ ./node_modules/webdriver-manager/bin/webdriver-manager start --versions.chrome '2.37' & \ ./scripts/env_vars.sh && \ diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 5a80a384809..00000000000 --- a/.travis.yml +++ /dev/null @@ -1,85 +0,0 @@ -language: node_js -node_js: 8.9.4 -env: - matrix: - - TEST=unit - - TEST=end-to-end - - TEST=api-sync - global: - - secure: 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 - - secure: 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 -before_install: -- if [[ `npm -v` != 5* ]]; then npm i -g npm@5.6.0; fi -install: -- npm config set registry https://registry.npmjs.org/ -- npm install -- npm install codecov.io -script: -- | - if [[ "${TEST}" == api-sync ]] - then - bash src/test/check_api_sync.sh - fi -- | - if [[ "${TEST}" == api-sync ]] - then - npm run syncmock || { \ - echo 'WARNING: mock data out of sync with API return calls'; - } - fi -- | - if [[ "${TEST}" == unit ]] - then - npm run build && \ - npm test - fi -- | - if [[ "${TEST}" == end-to-end ]] - then - npm run buildDLL:dev - fi - # Use browserstack only on runs within repo (use cbioportal.org for master & - # hotfix, cbioportal.org/beta for everything else) -- | - if [[ "${TEST}" == end-to-end && "${TRAVIS_PULL_REQUEST}" = "false" ]]; - then - npm run start & \ - eval "$(./scripts/env_vars.sh)" && \ - curl $CBIOPORTAL_URL > /dev/null && \ - sleep 5s && \ - curl $CBIOPORTAL_URL > /dev/null && \ - sleep 5s && \ - curl $CBIOPORTAL_URL > /dev/null && \ - sleep 20s && \ - curl http://localhost:3000 > /dev/null && \ - sleep 20s && \ - cd end-to-end-tests && \ - npm install && \ - npm run test-travis - fi - # run webdriver-manager on PRs instead of using browserstack - # not working atm - # - | - # if [[ "${TEST}" == end-to-end && "${TRAVIS_PULL_REQUEST}" != "false" ]]; - # then - # npm run start & \ - # npm install -g webdriver-manager@10.2.5 && \ - # webdriver-manager start & - # eval "$(./scripts/env_vars.sh)" && \ - # curl $CBIOPORTAL_URL > /dev/null && \ - # sleep 5s && \ - # curl $CBIOPORTAL_URL > /dev/null && \ - # sleep 5s && \ - # curl $CBIOPORTAL_URL > /dev/null && \ - # sleep 20s && \ - # curl http://localhost:3000 > /dev/null && \ - # sleep 20s && \ - # cd end-to-end-tests && \ - # npm install && \ - # npm run test-webdriver-manager - # fi -after_success: -- cat test/fixtures/outputs/lcov.info | codecov -cache: - directories: - - node_modules diff --git a/end-to-end-tests/screenshots/reference/'profiled_in'_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png b/end-to-end-tests/screenshots/reference/'profiled_in'_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png deleted file mode 100644 index ca647bda824..00000000000 Binary files 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files a/end-to-end-tests/screenshots/reference/session_network_tab_element_chrome_1600x1000.png and b/end-to-end-tests/screenshots/reference/session_network_tab_element_chrome_1600x1000.png differ diff --git a/end-to-end-tests/screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png b/end-to-end-tests/screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png index df0b2b7c7a5..0e991b28bce 100644 Binary files a/end-to-end-tests/screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png and b/end-to-end-tests/screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png differ diff --git a/end-to-end-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png b/end-to-end-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png index b589ed9c870..4b7d4312f38 100644 Binary files a/end-to-end-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png and b/end-to-end-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png differ diff --git a/end-to-end-tests/specs/screenshot.spec.js b/end-to-end-tests/specs/screenshot.spec.js index e6e50b99abd..d0fd61afca5 100644 --- a/end-to-end-tests/specs/screenshot.spec.js +++ b/end-to-end-tests/specs/screenshot.spec.js @@ -181,14 +181,14 @@ describe("oncoprint screenshot tests", function() { var res = browser.checkElement("#oncoprint"); assertScreenShotMatch(res); }); - it("'profiled in' tracks in msk impact with 3 n/p genes", function() { + it("profiled in tracks in msk impact with 3 not profiled genes", function() { var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=msk_impact_2017&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=msk_impact_2017_cnaseq&gene_list=AKR1C1%2520AKR1C2%2520AKR1C4&geneset_list=+&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=msk_impact_2017_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=msk_impact_2017_cna`; goToUrlAndSetLocalStorage(url); waitForOncoprint(20000); var res = browser.checkElement("#oncoprint"); assertScreenShotMatch(res); }); - it("'profiled in' tracks in multiple study with SOS1", function() { + it("profiled in tracks in multiple study with SOS1", function() { var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=all&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=all&gene_list=SOS1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&cancer_study_list=msk_impact_2017%2Cbrca_bccrc&show_samples=false&clinicallist=CANCER_STUDY%2CPROFILED_IN_MUTATION_EXTENDED%2CPROFILED_IN_msk_impact_2017_cna#summary`; goToUrlAndSetLocalStorage(url); waitForOncoprint(20000); diff --git a/package-lock.json b/package-lock.json index 66e62b7ae96..d1a65b586fa 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,21 +8,22 @@ "resolved": "https://registry.npmjs.org/3d-view/-/3d-view-2.0.0.tgz", "integrity": "sha1-gxrpQtdQjFCAHj4G+v4ejFdOF74=", "requires": { - "matrix-camera-controller": "2.1.3", - "orbit-camera-controller": "4.0.0", - "turntable-camera-controller": "3.0.1" + "matrix-camera-controller": "^2.1.1", + "orbit-camera-controller": "^4.0.0", + "turntable-camera-controller": "^3.0.0" } }, "3d-view-controls": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/3d-view-controls/-/3d-view-controls-2.2.0.tgz", - "integrity": "sha1-RK7JxEjCe+NLPdUR/5ICq2FQ3KU=", + "version": "2.2.2", + "resolved": "https://registry.npmjs.org/3d-view-controls/-/3d-view-controls-2.2.2.tgz", + "integrity": "sha512-WL0u3PN41lEx/4qvKqV6bJlweUYoW18FXMshW/qHb41AVdZxDReLoJNGYsI7x6jf9bYelEF62BJPQmO7yEnG2w==", "requires": { - "3d-view": "2.0.0", - "mouse-change": "1.4.0", - "mouse-event-offset": "3.0.2", - "mouse-wheel": "1.2.0", - "right-now": "1.0.0" + "3d-view": "^2.0.0", + "has-passive-events": "^1.0.0", + "mouse-change": "^1.1.1", + "mouse-event-offset": "^3.0.2", + "mouse-wheel": "^1.0.2", + "right-now": "^1.0.0" } }, "3dmol": { @@ -30,14 +31,85 @@ "resolved": "https://registry.npmjs.org/3dmol/-/3dmol-1.1.4.tgz", "integrity": "sha1-HdSXVZqMehUe163HSXbcBF0krvU=" }, + "@choojs/findup": { + "version": "0.2.1", + "resolved": "https://registry.npmjs.org/@choojs/findup/-/findup-0.2.1.tgz", + "integrity": "sha512-YstAqNb0MCN8PjdLCDfRsBcGVRN41f3vgLvaI0IrIcBp4AqILRSS0DeWNGkicC+f/zRIPJLc+9RURVSepwvfBw==", + "requires": { + "commander": "^2.15.1" + }, + "dependencies": { + "commander": { + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-2.19.0.tgz", + "integrity": "sha512-6tvAOO+D6OENvRAh524Dh9jcfKTYDQAqvqezbCW82xj5X0pSrcpxtvRKHLG0yBY6SD7PSDrJaj+0AiOcKVd1Xg==" + } + } + }, + "@mapbox/geojson-area": { + "version": "0.2.2", + "resolved": "https://registry.npmjs.org/@mapbox/geojson-area/-/geojson-area-0.2.2.tgz", + "integrity": "sha1-GNeBSqNr8j+7zDefjiaiKSfevxA=", + "requires": { + "wgs84": "0.0.0" + } + }, + "@mapbox/gl-matrix": { + "version": "0.0.1", + "resolved": "https://registry.npmjs.org/@mapbox/gl-matrix/-/gl-matrix-0.0.1.tgz", + "integrity": "sha1-5RJqq01kw2uBx6l9CuDd3eV3PSs=" + }, + "@mapbox/jsonlint-lines-primitives": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/@mapbox/jsonlint-lines-primitives/-/jsonlint-lines-primitives-2.0.2.tgz", + "integrity": "sha1-zlblOfg1UrWNENZy6k1vya3HsjQ=" + }, + "@mapbox/mapbox-gl-supported": { + "version": "1.4.0", + "resolved": "https://registry.npmjs.org/@mapbox/mapbox-gl-supported/-/mapbox-gl-supported-1.4.0.tgz", + "integrity": "sha512-ZD0Io4XK+/vU/4zpANjOtdWfVszAgnaMPsGR6LKsWh4kLIEv9qoobTVmJPPuwuM+ZI2b3BlZ6DYw1XHVmv6YTA==" + }, + "@mapbox/point-geometry": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/@mapbox/point-geometry/-/point-geometry-0.1.0.tgz", + "integrity": "sha1-ioP5M1x4YO/6Lu7KJUMyqgru2PI=" + }, + "@mapbox/shelf-pack": { + "version": "3.2.0", + "resolved": "https://registry.npmjs.org/@mapbox/shelf-pack/-/shelf-pack-3.2.0.tgz", + "integrity": "sha512-dyQxe6ukILV6qaEvxoKCIwhblgRjYp1ZGlClo4xvfbmxzFO5LYu7Tnrg2AZrRgN7VsSragsGcNjzUe9kCdKHYQ==" + }, + "@mapbox/tiny-sdf": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/@mapbox/tiny-sdf/-/tiny-sdf-1.1.0.tgz", + "integrity": "sha512-dnhyk8X2BkDRWImgHILYAGgo+kuciNYX30CUKj/Qd5eNjh54OWM/mdOS/PWsPeN+3abtN+QDGYM4G220ynVJKA==" + }, + "@mapbox/unitbezier": { + "version": "0.0.0", + "resolved": "https://registry.npmjs.org/@mapbox/unitbezier/-/unitbezier-0.0.0.tgz", + "integrity": "sha1-FWUb1VOme4WB+zmIEMmK2Go0Uk4=" + }, + "@mapbox/vector-tile": { + "version": "1.3.1", + "resolved": "https://registry.npmjs.org/@mapbox/vector-tile/-/vector-tile-1.3.1.tgz", + "integrity": "sha512-MCEddb8u44/xfQ3oD+Srl/tNcQoqTw3goGk2oLsrFxOTc3dUp+kAnby3PvAeeBYSMSjSPD1nd1AJA6W49WnoUw==", + "requires": { + "@mapbox/point-geometry": "~0.1.0" + } + }, + "@mapbox/whoots-js": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/@mapbox/whoots-js/-/whoots-js-3.1.0.tgz", + "integrity": "sha512-Es6WcD0nO5l+2BOQS4uLfNPYQaNDfbot3X1XUoloz+x0mPDS3eeORZJl06HXjwBG1fOGwCRnzK88LMdxKRrd6Q==" + }, "@plotly/d3-sankey": { "version": "0.5.0", "resolved": "https://registry.npmjs.org/@plotly/d3-sankey/-/d3-sankey-0.5.0.tgz", "integrity": "sha1-si+up0LlglEzXuXZ+6JIdyYHgA8=", "requires": { - "d3-array": "1.2.0", - "d3-collection": "1.0.4", - "d3-interpolate": "1.1.5" + "d3-array": "1", + "d3-collection": "1", + "d3-interpolate": "1" } }, "@types/chai": { @@ -50,10 +122,10 @@ "resolved": "https://registry.npmjs.org/@types/chai-enzyme/-/chai-enzyme-0.6.2.tgz", "integrity": "sha512-Tq34TSo06qM9h0XoQOoV+yvNAP4z2KQRStbv8suk0uNS2fOTW0RaykMvHxnFdIW2r2444KFIyh0vHuLn7buZow==", "requires": { - "@types/chai": "3.5.2", - "@types/cheerio": "0.22.2", - "@types/enzyme": "2.8.0", - "@types/react": "15.6.2" + "@types/chai": "*", + "@types/cheerio": "*", + "@types/enzyme": "*", + "@types/react": "*" } }, "@types/chart.js": { @@ -61,7 +133,7 @@ "resolved": "https://registry.npmjs.org/@types/chart.js/-/chart.js-2.6.3.tgz", "integrity": "sha512-XX7fP4h4kxeZbSVfPWTyt/3fgem4TCr6psQgk5QAKnQVXPUwtOYuKeVJwvov38FNHsKvBIBS6m2454YdjbcxVw==", "requires": { - "@types/jquery": "2.0.46" + "@types/jquery": "*" } }, "@types/cheerio": { @@ -79,7 +151,7 @@ "resolved": "https://registry.npmjs.org/@types/d3-scale/-/d3-scale-2.0.1.tgz", "integrity": "sha512-D5ZWv8ToLvqacE7XkdMNHMiiVDULdDxT7FMMGU0YJC3/nVzBmApjyTyxracUWOQyY3KK7YhZ05on8pOcNi0dfQ==", "requires": { - "@types/d3-time": "1.0.8" + "@types/d3-time": "*" } }, "@types/d3-time": { @@ -97,8 +169,8 @@ "resolved": "https://registry.npmjs.org/@types/enzyme/-/enzyme-2.8.0.tgz", "integrity": "sha1-hMYgTPiYMSI6iattw/SQseCIY1I=", "requires": { - "@types/cheerio": "0.22.2", - "@types/react": "15.6.2" + "@types/cheerio": "*", + "@types/react": "*" } }, "@types/history": { @@ -126,7 +198,7 @@ "resolved": "https://registry.npmjs.org/@types/jstree/-/jstree-3.3.35.tgz", "integrity": "sha512-heQHQbohuKOwLrM5VnfaXV71bCd3Th5FT5MFn5yoJtx6ivyPEIkY1Hi8SBhq1PWFOl+YBEFUaSNAvxVdDBzgsQ==", "requires": { - "@types/jquery": "2.0.46" + "@types/jquery": "*" } }, "@types/lodash": { @@ -169,7 +241,7 @@ "resolved": 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"integrity": "sha1-OoBuEPLaa6v+pBNr5lEOibDXaQE=", "requires": { - "classnames": "2.2.5" + "classnames": "^2.2.5" } }, "react-element-to-jsx-string": { @@ -14626,12 +14481,12 @@ "integrity": "sha1-xmOkgAqccSEVwNhRnLAhWkah8PI=", "dev": true, "requires": { - "collapse-white-space": "1.0.3", - "is-plain-object": "2.0.4", - "lodash": "4.17.4", - "sortobject": "1.1.1", + "collapse-white-space": "^1.0.0", + "is-plain-object": "^2.0.1", + "lodash": "^4.17.4", + "sortobject": "^1.0.0", "stringify-object": "2.4.0", - "traverse": "0.6.6" + "traverse": "^0.6.6" } }, "react-fast-compare": { @@ -14649,7 +14504,7 @@ "resolved": "https://registry.npmjs.org/react-fontawesome/-/react-fontawesome-1.6.1.tgz", "integrity": "sha1-7dzhfn3HMaoJ/UoYZoimF5OhbFw=", "requires": { - "prop-types": "15.5.10" + "prop-types": "^15.5.6" } }, "react-github-fork-ribbon": { @@ -14671,8 +14526,8 @@ "resolved": "https://registry.npmjs.org/create-react-class/-/create-react-class-15.5.2.tgz", "integrity": 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"0.1.2", + "forwarded": "~0.1.2", "ipaddr.js": "1.5.2" } }, @@ -19247,18 +19530,18 @@ "dev": true, "requires": { "debug": "2.6.9", - "depd": "1.1.1", - "destroy": "1.0.4", - "encodeurl": "1.0.1", - "escape-html": "1.0.3", - "etag": "1.8.1", + "depd": "~1.1.1", + "destroy": "~1.0.4", + "encodeurl": "~1.0.1", + "escape-html": "~1.0.3", + "etag": "~1.8.1", "fresh": "0.5.2", - "http-errors": "1.6.2", + "http-errors": "~1.6.2", "mime": "1.4.1", "ms": "2.0.0", - "on-finished": "2.3.0", - "range-parser": "1.2.0", - "statuses": "1.3.1" + "on-finished": "~2.3.0", + "range-parser": "~1.2.0", + "statuses": "~1.3.1" }, "dependencies": { "debug": { @@ -19278,9 +19561,9 @@ "integrity": "sha512-hSMUZrsPa/I09VYFJwa627JJkNs0NrfL1Uzuup+GqHfToR2KcsXFymXSV90hoyw3M+msjFuQly+YzIH/q0MGlQ==", "dev": true, "requires": { - "encodeurl": "1.0.1", - "escape-html": "1.0.3", - "parseurl": "1.3.2", + "encodeurl": "~1.0.1", + "escape-html": "~1.0.3", + "parseurl": "~1.3.2", "send": "0.16.1" } }, @@ -19296,7 +19579,7 @@ "integrity": "sha1-vnoN5ITexcXN34s9WRJQRJEvY1s=", "dev": true, "requires": { - "has-flag": "2.0.0" + "has-flag": "^2.0.0" } }, "utils-merge": { @@ -19327,7 +19610,8 @@ }, "dependencies": { "eve": { - "version": "git://github.com/adobe-webplatform/eve.git#eef80ed8d188423c2272746fb8ae5cc8dad84cb1" + "version": "git://github.com/adobe-webplatform/eve.git#eef80ed8d188423c2272746fb8ae5cc8dad84cb1", + "from": "eve@git://github.com/adobe-webplatform/eve.git#eef80ed8d188423c2272746fb8ae5cc8dad84cb1" } } }, @@ -19336,8 +19620,8 @@ "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-1.1.0.tgz", "integrity": "sha512-aqYp18kPphgoO5c/+NaUvEeACtZjMESmDChuD3NBciVpah3XpMEU9VAAtIaB1BsfJWWTSdv8Vv1m3T0aRk2dUw==", "requires": { - "source-list-map": "2.0.0", - "source-map": "0.6.1" + "source-list-map": "^2.0.0", + "source-map": "~0.6.1" }, "dependencies": { "source-list-map": { @@ -19358,8 +19642,8 @@ "integrity": "sha1-DK+dLXVdk67gSdS90NP+LMoqJOs=", "dev": true, "requires": { - "http-parser-js": "0.4.9", - "websocket-extensions": "0.1.3" + "http-parser-js": ">=0.4.0", + "websocket-extensions": ">=0.1.1" } }, "websocket-extensions": { @@ -19368,11 +19652,6 @@ "integrity": "sha512-nqHUnMXmBzT0w570r2JpJxfiSD1IzoI+HGVdd3aZ0yNi3ngvQ4jv1dtHt5VGxfI2yj5yqImPhOK4vmIh2xMbGg==", "dev": true }, - "webworkify": { - "version": "1.5.0", - "resolved": "https://registry.npmjs.org/webworkify/-/webworkify-1.5.0.tgz", - "integrity": "sha512-AMcUeyXAhbACL8S2hqqdqOLqvJ8ylmIbNwUIqQujRSouf4+eUFaXbG6F1Rbu+srlJMmxQWsiU7mOJi0nMBfM1g==" - }, "wgs84": { "version": "0.0.0", "resolved": "https://registry.npmjs.org/wgs84/-/wgs84-0.0.0.tgz", @@ -19393,7 +19672,7 @@ "resolved": "https://registry.npmjs.org/which/-/which-1.3.0.tgz", "integrity": "sha512-xcJpopdamTuY5duC/KnTTNBraPK54YwpenP4lzxU8H91GudWpFv38u0CKjclE1Wi2EH2EDz5LRcHcKbCIzqGyg==", "requires": { - "isexe": "2.0.0" + "isexe": "^2.0.0" } }, "which-module": { @@ -19401,17 +19680,12 @@ "resolved": "https://registry.npmjs.org/which-module/-/which-module-1.0.0.tgz", "integrity": "sha1-u6Y8qGGUiZT/MHc2CJ47lgJsKk8=" }, - "whoots-js": { - "version": "2.1.0", - "resolved": "https://registry.npmjs.org/whoots-js/-/whoots-js-2.1.0.tgz", - "integrity": "sha1-vLIBw04OrzNfzOWuLPh0V5qZxIc=" - }, "wide-align": { - "version": "1.1.2", - "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.2.tgz", - "integrity": "sha512-ijDLlyQ7s6x1JgCLur53osjm/UXUYD9+0PbYKrBsYisYXzCxN+HC3mYDNy/dWdmf3AwqwU3CXwDCvsNgGK1S0w==", + "version": "1.1.3", + "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.3.tgz", + "integrity": "sha512-QGkOQc8XL6Bt5PwnsExKBPuMKBxnGxWWW3fU55Xt4feHozMUhdUMaBCk290qpm/wG5u/RSKzwdAC4i51YigihA==", "requires": { - "string-width": "1.0.2" + "string-width": "^1.0.2 || 2" } }, "window-size": { @@ -19435,7 +19709,7 @@ "resolved": "https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.3.tgz", "integrity": "sha1-slxQMrokEo/8QdCfr0pewbnBQzU=", "requires": { - "object-assign": "4.1.1" + "object-assign": "^4.1.0" } }, "wrap-ansi": { @@ -19443,8 +19717,8 @@ "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz", "integrity": "sha1-2Pw9KE3QV5T+hJc8rs3Rz4JP3YU=", "requires": { - "string-width": "1.0.2", - "strip-ansi": "3.0.1" + "string-width": "^1.0.1", + "strip-ansi": "^3.0.1" } }, "wrappy": { @@ -19458,7 +19732,7 @@ "integrity": "sha1-X8A4KOJkzqP+kUVUdvejxWbLB1c=", "dev": true, "requires": { - "mkdirp": "0.5.1" + "mkdirp": "^0.5.1" } }, "ws": { @@ -19467,8 +19741,8 @@ "integrity": "sha1-iiRPoFJAHgjJiGz0SoUYnh/UBn8=", "dev": true, "requires": { - "options": "0.0.6", - "ultron": "1.0.2" + "options": ">=0.0.5", + "ultron": "1.0.x" } }, "wtf-8": { @@ -19477,11 +19751,6 @@ "integrity": "sha1-OS2LotDxw00e4tYw8V0O+2jhBIo=", "dev": true }, - "xml-char-classes": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/xml-char-classes/-/xml-char-classes-1.0.0.tgz", - "integrity": "sha1-ZGV4SKIP/F31g6Qq2KJ3tFErvE0=" - }, "xmlbuilder": { "version": "8.2.2", "resolved": "https://registry.npmjs.org/xmlbuilder/-/xmlbuilder-8.2.2.tgz", @@ -19514,19 +19783,19 @@ "resolved": "https://registry.npmjs.org/yargs/-/yargs-6.6.0.tgz", "integrity": "sha1-eC7CHvQDNF+DCoCMo9UTr1YGUgg=", "requires": { - "camelcase": "3.0.0", - "cliui": "3.2.0", - "decamelize": "1.2.0", - "get-caller-file": "1.0.2", - "os-locale": "1.4.0", - "read-pkg-up": "1.0.1", - "require-directory": "2.1.1", - "require-main-filename": "1.0.1", - "set-blocking": "2.0.0", - "string-width": "1.0.2", - "which-module": "1.0.0", - "y18n": "3.2.1", - "yargs-parser": "4.2.1" + "camelcase": "^3.0.0", + "cliui": "^3.2.0", + "decamelize": "^1.1.1", + "get-caller-file": "^1.0.1", + "os-locale": "^1.4.0", + "read-pkg-up": "^1.0.1", + "require-directory": "^2.1.1", + "require-main-filename": "^1.0.1", + "set-blocking": "^2.0.0", + "string-width": "^1.0.2", + "which-module": "^1.0.0", + "y18n": "^3.2.1", + "yargs-parser": "^4.2.0" }, "dependencies": { "camelcase": { @@ -19539,7 +19808,7 @@ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-4.2.1.tgz", "integrity": "sha1-KczqwNxPA8bIe0qfIX3RjJ90hxw=", "requires": { - "camelcase": "3.0.0" + "camelcase": "^3.0.0" } } } @@ -19549,7 +19818,7 @@ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-5.0.0.tgz", "integrity": "sha1-J17PDX/+Bcd+ZOfIbkzZS/DhIoo=", "requires": { - "camelcase": "3.0.0" + "camelcase": "^3.0.0" }, "dependencies": { "camelcase": { @@ -19565,7 +19834,7 @@ "integrity": "sha1-lSj0QtqxsihOWLQ3m7GU4i4MQAU=", "dev": true, "requires": { - "fd-slicer": "1.0.1" + "fd-slicer": "~1.0.1" } }, "yeast": { @@ -19579,7 +19848,7 @@ "resolved": "https://registry.npmjs.org/zero-crossings/-/zero-crossings-1.0.1.tgz", "integrity": "sha1-xWK9MRNkPzRDokXRJAa4i2m5qf8=", "requires": { - "cwise-compiler": "1.1.3" + "cwise-compiler": "^1.0.0" } } } diff --git a/package.json b/package.json index b967090333e..1b5ee923d8e 100644 --- a/package.json +++ b/package.json @@ -32,8 +32,8 @@ "validate": "npm ls" }, "engines": { - "npm": "5.6.0", - "node": "8.9.4" + "npm": "6.4.1", + "node": "8.12.0" }, "author": "", "license": "", @@ -78,7 +78,7 @@ "addthis-snippet": "^1.0.1", "autobind-decorator": "^2.1.0", "autoprefixer": "^6.7.0", - "babel-core": "^6.22.1", + "babel-core": "^6.26.3", "babel-loader": "^6.2.10", "babel-plugin-transform-es2015-modules-umd": "^6.22.0", "babel-polyfill": "^6.22.0", @@ -107,7 +107,7 @@ "d3-scale": "^2.0.0", "datatables.net": "^1.10.13", "dotenv": "^4.0.0", - "express": "^4.14.0", + "express": "^4.16.4", "extract-text-webpack-plugin": "^2.1.2", "file-loader": "^0.9.0", "fixed-data-table": "^0.6.3", @@ -128,7 +128,7 @@ "jstree": "^3.3.4", "less": "^2.7.2", "loader-utils": "^1.0.2", - "lodash": "^4.17.4", + "lodash": "^4.17.11", "lolex": "^1.6.0", "measure-text": "0.0.4", "memoize-weak-decorator": "^1.0.3", @@ -139,12 +139,12 @@ "mobx-react-router": "^3.1.2", "mobx-utils": "^2.0.1", "mobxpromise": "^1.3.1", - "node-sass": "^4.3.0", + "node-sass": "^4.9.3", "numeral": "^2.0.6", "oncoprintjs": "^1.1.6", "parameter-validator": "^1.0.2", "pdfobject": "^2.0.201604172", - "plotly.js": "^1.31.2", + "plotly.js": "^1.41.3", "postcss-loader": "^1.2.2", "precss": "^1.4.0", "progress-bar-webpack-plugin": "^1.9.3", @@ -207,7 +207,7 @@ "seedrandom": "^2.4.3", "source-map-loader": "^0.1.6", "style-loader": "^0.13.1", - "superagent": "^3.4.0", + "superagent": "^3.8.3", "swagger-client": "^2.1.32", "ts-loader": "^2.0.0", "typescript": "^2.7.2", @@ -232,7 +232,7 @@ "enzyme": "2.8.0", "eslint": "^3.14.1", "eslint-config-airbnb": "^14.0.0", - "eslint-plugin-import": "^2.2.0", + "eslint-plugin-import": "^2.14.0", "eslint-plugin-jsx-a11y": "^3.0.2", "eslint-plugin-react": "^6.9.0", "expect": "^1.20.2", @@ -243,7 +243,7 @@ "karma": "^1.7.0", "karma-chai": "^0.1.0", "karma-chrome-launcher": "^2.2.0", - "karma-coverage": "^1.1.1", + "karma-coverage": "^1.1.2", "karma-coverage-es6": "^0.2.7", "karma-coverage-istanbul-reporter": "^0.2.0", "karma-jasmine": "^1.1.0", @@ -255,11 +255,11 @@ "karma-webpack": "^2.0.2", "mocha": "^3.2.0", "phantomjs-polyfill": "^0.0.2", - "phantomjs-prebuilt": "^2.1.14", - "redux-devtools": "^3.3.2", + "phantomjs-prebuilt": "^2.1.16", + "redux-devtools": "^3.4.1", "redux-devtools-dock-monitor": "^1.1.1", "redux-devtools-log-monitor": "^1.2.0", - "request": "^2.79.0", + "request": "^2.88.0", "sinon": "^4.1.3", "swagger-js-codegen": "git+https://github.com/cBioPortal/swagger-js-codegen.git#9884320556205139992530835bcf985dcc80cfcc", "tslint": "^5.2.0", diff --git a/pom.xml b/pom.xml index b14faf4a28f..b7feb248973 100644 --- a/pom.xml +++ b/pom.xml @@ -24,8 +24,8 @@ - v8.9.4 - 5.6.0 + v8.12.0 + 6.4.1 @@ -36,7 +36,7 @@ - install --production + ci --only=production