fix(dependencies): Bump cornerstone-tools to 3.11.0 (#497)

Fix codesandbox link

.all-contributorsrc

@@ -0,0 +1,68 @@
+{
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "contributors": [
+    {
+      "login": "swederik",
+      "name": "Erik Ziegler",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/607793?v=4",
+      "profile": "https://github.com/swederik",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "evren217",
+      "name": "Evren Ozkan",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/4920551?v=4",
+      "profile": "https://github.com/evren217",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "galelis",
+      "name": "Gustavo André Lelis",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/2378326?v=4",
+      "profile": "https://github.com/galelis",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "dannyrb",
+      "name": "Danny Brown",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/5797588?v=4",
+      "profile": "http://dannyrb.com/",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "allcontributors",
+      "name": "allcontributors[bot]",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/46843839?v=4",
+      "profile": "https://github.com/all-contributors/all-contributors-bot",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "EsrefDurna",
+      "name": "Esref Durna",
+      "avatar_url": "https://avatars0.githubusercontent.com/u/1230575?v=4",
+      "profile": "https://www.linkedin.com/in/siliconvalleynextgeneration/",
+      "contributions": [
+        "question"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7,
+  "projectName": "Viewers",
+  "projectOwner": "OHIF",
+  "repoType": "github",
+  "repoHost": "https://github.com"
+}

.babelrc

@@ -0,0 +1,19 @@
+{
+  "presets": [
+    [
+      "@babel/preset-env",
+      {
+        "targets": {
+          "ie": "11"
+        }
+      }
+    ],
+    "@babel/preset-react"
+  ],
+  "plugins": [
+    "@babel/plugin-proposal-class-properties",
+    "@babel/plugin-syntax-dynamic-import",
+    "@babel/plugin-transform-regenerator",
+    "@babel/plugin-transform-runtime"
+  ]
+}

.circleci/config.yml

@@ -0,0 +1,155 @@
+version: 2
+
+### ABOUT
+#
+# This configuration powers our Circleci.io integration
+#
+# Note:
+# Netlify works independently from this configuration to
+# create pull request previews and to update `https://docs.ohif.org`
+###
+
+defaults: &defaults
+  working_directory: ~/repo
+  docker:
+    - image: circleci/node:10.15.1
+
+jobs:
+  build_and_test:
+    <<: *defaults
+    steps:
+      # Download and cache dependencies
+      - checkout
+      - restore_cache:
+          name: Restore Yarn Package Cache
+          keys:
+            # when lock file changes, use increasingly general patterns to restore cache
+            - yarn-packages-v1-{{ .Branch }}-{{ checksum "yarn.lock" }}
+            - yarn-packages-v1-{{ .Branch }}-
+            - yarn-packages-v1-
+      - run:
+          name: Install Dependencies
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache/yarn
+          key: yarn-packages-v1-{{ .Branch }}-{{ checksum "yarn.lock" }}
+      # Build & Test
+      - run: yarn build:package:ci
+      # https://www.viget.com/articles/using-junit-on-circleci-2-0-with-jest-and-eslint/
+      - run:
+          name: 'JavaScript Test Suite'
+          command: yarn test:ci
+          environment:
+            JEST_JUNIT_OUTPUT: 'reports/junit/js-test-results.xml'
+      # Store result
+      - store_test_results:
+          path: reports/junit
+      - store_artifacts:
+          path: reports/junit
+      # Persist :+1:
+      - persist_to_workspace:
+          root: ~/repo
+          paths: .
+
+  npm_publish:
+    <<: *defaults
+    steps:
+      - attach_workspace:
+          at: ~/repo
+      - run:
+          name: Avoid hosts unknown for github
+          command:
+            mkdir ~/.ssh/ && echo -e "Host github.com\n\tStrictHostKeyChecking
+            no\n" > ~/.ssh/config
+      # --no-ci argument is not ideal; however, semantic-rlease thinks we're
+      # attempting to run it from a `pr`, which is not the case
+      - run:
+          name: Publish using Semantic Release
+          command: npx semantic-release --debug
+      # Persist :+1:
+      - persist_to_workspace:
+          root: ~/repo
+          paths: .
+
+  docs_publish:
+    <<: *defaults
+    steps:
+      - attach_workspace:
+          at: ~/repo
+      - run:
+          name: Avoid hosts unknown for github
+          command:
+            mkdir ~/.ssh/ && echo -e "Host github.com\n\tStrictHostKeyChecking
+            no\n" > ~/.ssh/config
+      - run: git config --global user.email "gh-pages@localhost"
+      - run: git config --global user.name "npm gh-pages"
+      - run: yarn global add gh-pages
+      - run:
+          name: Generate Docs
+          command: yarn run staticDeploy
+      - run:
+          name: Publish Docs
+          command: yarn run docs:publish
+
+  docker_publish:
+    <<: *defaults
+    steps:
+      - attach_workspace:
+          at: ~/repo
+      - setup_remote_docker:
+          docker_layer_caching: true
+      - run:
+          name: Build and push Docker image
+          command: |
+            # This file will exist if a new version was published by
+            # our `semantic-release` command in the previous job
+            if [[ ! -e tmp/updated-version.txt ]]; then
+              exit 0
+            else
+              # Remove npm config
+              rm -f ./.npmrc
+              # Set our version number using vars
+              export IMAGE_VERSION=$(cat tmp/updated-version.txt)
+              export IMAGE_VERSION_FULL=v$IMAGE_VERSION.${CIRCLE_BUILD_NUM}
+              echo $IMAGE_VERSION
+              echo $IMAGE_VERSION_FULL
+              # Build our image, auth, and push
+              docker build --tag ohif/$IMAGE_NAME:$IMAGE_VERSION_FULL --tag ohif/$IMAGE_NAME:latest .
+              echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
+              docker push ohif/$IMAGE_NAME:$IMAGE_VERSION_FULL
+              docker push ohif/$IMAGE_NAME:latest
+            fi
+
+workflows:
+  version: 2
+
+  # PULL REQUESTS
+  pull_requests:
+    jobs:
+      - build_and_test:
+          filters:
+            branches:
+              ignore:
+                - master
+                - feature/*
+                - hotfix/*
+
+  # MERGE TO MASTER
+  cut_release:
+    jobs:
+      - build_and_test:
+          filters:
+            branches:
+              only: master
+      - npm_publish:
+          requires:
+            - build_and_test
+      - docs_publish:
+          requires:
+            - build_and_test
+      - docker_publish:
+          requires:
+            - build_and_test
+            - npm_publish

.dockerignore

@@ -1,17 +1,16 @@
-.idea/
-.meteor/local
-.meteor/meteorite
-.meteor/dev_bundle
-*/.meteor/dev_bundle
-node_modules
-.npm
-npm-debug.log
-Packages/active-entry/helloworld/
-LesionTracker/tests/nightwatch/reports/
-package-lock.json
-docs/_book
-docs/
-img/
-test/
-LesionTracker/
-StandaloneViewer/
+# Output
+dist/
+
+# Dependencies
+node_modules/
+
+# Root
+README.md
+Dockerfile
+
+# Misc. Config
+.git
+.DS_Store
+.gitignore
+.vscode
+.circleci

.env

@@ -0,0 +1,14 @@
+##
+# Environment: Default
+#
+# We're using this to set variables for development.
+# Please feel free to delete or modify this file for your own setup.
+# Be careful not to commit anything sensitive to source control.
+#
+
+PUBLIC_URL=/
+
+#
+# Most vars require REACT_APP_* naming
+#
+REACT_APP_CONFIG=config/default.js

.env.example

@@ -0,0 +1,13 @@
+##
+# EXAMPLE
+#
+# Read more about .env files when using create-react-app here:
+# https://facebook.github.io/create-react-app/docs/adding-custom-environment-variables#adding-development-environment-variables-in-env
+#
+
+PUBLIC_URL=/demo
+
+#
+# Most vars require REACT_APP_* naming
+#
+REACT_APP_CONFIG=config/netlify.js

.eslintignore

@@ -1,4 +1,3 @@
 config/**
 docs/**
 img/**
-StandaloneViewer/**

.eslintrc

@@ -0,0 +1,16 @@
+{
+  "extends": [
+    "react-app",
+    "eslint:recommended",
+    "plugin:react/recommended"
+  ],
+  "parser": "babel-eslint",
+  "env": {
+    "jest": true
+  },
+  "settings": {
+    "react": {
+      "version": "detect",
+    },
+  },
+}

.eslintrc.js

@@ -1,16 +0,0 @@
-module.exports = {
-  'env': {
-    'browser': true,
-    'es6': true,
-    'jquery': true,
-    'node': true,
-    'mocha': true
-  },
-  'extends': 'eslint:recommended',
-  'parserOptions': {
-    'sourceType': 'module'
-  },
-  'rules': {
-    'no-undef': 'error',
-  }
-};

.gitignore

@@ -1,11 +1,27 @@
-.idea/
-.meteor/local
-.meteor/meteorite
-.meteor/dev_bundle
-*/.meteor/dev_bundle
+# Packages
 node_modules
+
+# Output
+build
+dist
+docs/_book
+src/version.js
+junit.xml
+coverage/
+
+# YALC (for Erik)
+.yalc
+yalc.lock
+
+# Logging, System files, misc.
+.idea/
 .npm
 npm-debug.log
-Packages/active-entry/helloworld/
-LesionTracker/tests/nightwatch/reports/
-docs/_book
+package-lock.json
+yarn-error.log
+.DS_Store
+
+# Common Example Data Directories
+sampledata/
+example/deps/
+docker/dcm4che/dcm4che-arc

.prettierrc

@@ -0,0 +1,9 @@
+{
+  "trailingComma": "es5",
+  "printWidth": 80,
+  "proseWrap": "always",
+  "tabWidth": 2,
+  "semi": false,
+  "singleQuote": true,
+  "endOfLine": "lf"
+}

.releaserc

@@ -0,0 +1,14 @@
+{
+  "plugins": [
+    "@semantic-release/commit-analyzer",
+    "@semantic-release/release-notes-generator",
+    "@semantic-release/npm",
+    "@semantic-release/github",
+    [
+      "@semantic-release/exec",
+      {
+        "publishCmd": "mkdir tmp && echo ${nextRelease.version} > tmp/updated-version.txt"
+      }
+    ]
+  ]
+}

.travis.yml

@@ -1,123 +0,0 @@
-language: node_js
-
-node_js:
-  - "lts/*"
-
-services:
-  - docker
-
-before_script:
-  - export PATH=$HOME/.meteor:$PATH
-
-cache:
-  directories:
-    - ~/.meteor
-    - node_modules
-    - OHIFViewer/node_modules
-
-env:
-  global:
-    - METEOR_PACKAGE_DIRS=../Packages
-    - secure: "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" # DOCKER_USER
-    - secure: "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" # DOCKER_PASS
-    - secure: "G5qjTBS6CuCCtueEqCRAEUhznycGz2kRXB7nChUK/ftKbAMW6F487sj8uujDEO0CXTv9aWnKyrPoXPnhlB5APQ5PtmC8F8DJEqWGW29J/oBv1giJq2K2Elcz6a0a7ys8pTgGKJyDT+mEvFF9boxVKI/eZQ+4ACI0EkGHBakpzey7Y1YSMsymtG6eM3ic1Fgrxna8FynzazKS0YdoE5Aj6yPDVpfj/7vSucz3wR3r2JxMtq95hiWKWYPdc/iir0dcDnedU+MF9aaAUv+ReHpM6FPScnan4mqOhrYKK5sBx27p0C/IxJhtaB4RVzU2F0kYLynK1vgUOBFc+9H/G2P+wl6TfO5dGjMmGU6kF2eWtTzRqT7JELRdqu9v/QGOlKpKmhmA3diGfkY0E2keEUyIRchHZAZKYQfLUhUObYcve2/4skmg9qhcxSMuh2qjkfTyFj/M4mcfkTZZWB9izgkHO2O3MxQm1d5DJDtoSfNQZOZiLjckyxmghWF3TEKNp3OhDOt+JikrDboZBts3F9+ocAVjLyg3upmWnlE6rFfkmVtWCXmI6Rto+laHtV/ng83Z3M4wL3VcvoOlPXLb0moqCGN4HGvpfolBqryFksGbUybaIqbQ7hQHhQuThzQ9UHq0AQN44rwzxEuKbxY7bTuyb4vSEAkrvjeLFbz4MSHQgno=" # AWS_ACCESS_KEY_ID
-    - secure: "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" # AWS_SECRET_ACCESS_KEY
-    - secure: "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" # GITHUB_TOKEN
-
-jobs:
-  include:
-    - stage: build production docker image
-      before_script:
-        - export REPO=ohif/viewer
-        - export COMMIT=${TRAVIS_COMMIT::8}
-        - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
-        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
-        - export TAG=`if [ "$TRAVIS_BRANCH" == "master" ]; then echo "latest"; else echo $TRAVIS_BRANCH ; fi`
-        - echo "TAG=$TAG, COMMIT=$COMMIT"
-        - docker pull $REPO:latest
-        - docker --version
-      script:
-        - docker build -t $REPO:$COMMIT . --cache-from $REPO:latest
-      after_success:
-        - docker tag $REPO:$COMMIT $REPO:$TAG
-        - docker tag $REPO:$COMMIT $REPO:travis-$TRAVIS_BUILD_NUMBER
-        - docker images
-        - docker login -u $DOCKER_USER -p $DOCKER_PASS
-        - docker push $REPO:$TAG
-        - docker push $REPO:travis-$TRAVIS_BUILD_NUMBER
-        - docker push $REPO:$COMMIT
-
-    - stage: build development docker image
-      before_script:
-        - export REPO=ohif/viewer-dev
-        - export COMMIT=${TRAVIS_COMMIT::8}
-        - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
-        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
-        - export TAG=`if [ "$TRAVIS_BRANCH" == "master" ]; then echo "latest"; else echo $TRAVIS_BRANCH ; fi`
-        - echo "TAG=$TAG, COMMIT=$COMMIT"
-        - docker pull $REPO:latest
-        - docker --version
-      script:
-        - docker build -f development.Dockerfile -t $REPO:$COMMIT . --cache-from $REPO:latest
-      after_success:
-        - docker tag $REPO:$COMMIT $REPO:$TAG
-        - docker tag $REPO:$COMMIT $REPO:travis-$TRAVIS_BUILD_NUMBER
-        - docker images
-        - docker login -u $DOCKER_USER -p $DOCKER_PASS
-        - docker push $REPO:$TAG
-        - docker push $REPO:travis-$TRAVIS_BUILD_NUMBER
-        - docker push $REPO:$COMMIT
-
-    - stage: build standalone viewer
-      if: branch = master
-      before_script:
-        - export ROOT_URL=http://ohif-viewer.s3-website.eu-central-1.amazonaws.com
-        - export METEOR_PACKAGE_DIRS="../../Packages"
-        - cd StandaloneViewer
-        - mkdir buildDirectory
-        - cd StandaloneViewer
-        - npm install -g meteor-build-client-fixed@0.4.3
-        - meteor-build-client-fixed --version
-        - curl https://install.meteor.com | /bin/sh
-        - meteor npm install
-      script:
-        - meteor-build-client-fixed ~/standaloneViewerBuild -u $ROOT_URL
-      after_success:
-        - ls ~/standaloneViewerBuild
-        - ls /home/travis
-        - ls /home/travis/build
-        - ls /home/travis/build/Viewers/StandaloneViewer
-      deploy:
-        provider: s3
-        access_key_id: $AWS_ACCESS_KEY_ID
-        secret_access_key: $AWS_SECRET_ACCESS_KEY
-        bucket: ohif-viewer
-        region: eu-central-1
-        skip_cleanup: true
-        local_dir: /home/travis/standaloneViewerBuild
-        acl: public_read
-        on:
-          branch: master
-
-    - stage: build documentation
-      if: branch = master
-      before_script:
-        - cd docs
-        - rm -rf _book
-        - npm install
-        - npm install -g gitbook-cli
-        - gitbook install
-      script:
-        - gitbook build
-      after_success:
-        - cp assets/CNAME _book/CNAME
-      deploy:
-        provider: pages
-        skip-cleanup: true
-        local-dir: docs/_book
-        github-token: $GITHUB_TOKEN
-        keep-history: true
-        fqdn: docs.ohif.org
-        verbose: true
-        on:
-          branch: master

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+  "recommendations": [
+    "esbenp.prettier-vscode",
+    "sysoev.language-stylus",
+    "dbaeumer.vscode-eslint",
+    "mikestead.dotenv"
+  ]
+}

.vscode/settings.json

@@ -0,0 +1,30 @@
+{
+    "editor.rulers": [80, 120],
+  
+    // ===
+    // Spacing
+    // ===
+  
+    "editor.insertSpaces": true,
+    "editor.tabSize": 2,
+    "editor.trimAutoWhitespace": true,
+    "files.trimTrailingWhitespace": true,
+    "files.eol": "\n",
+    "files.insertFinalNewline": true,
+    "files.trimFinalNewlines": true,
+  
+    // ===
+    // Event Triggers
+    // ===
+  
+    "editor.formatOnSave": true,
+    "eslint.autoFixOnSave": true,
+    "eslint.run": "onSave",
+    "eslint.validate": [
+      { "language": "javascript", "autoFix": true },
+      { "language": "javascriptreact", "autoFix": true }
+    ],
+    "prettier.disableLanguages": [],
+    "prettier.endOfLine": "lf"
+  }
+  

LICENSE

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

LesionTracker/.eslintrc.json

@@ -1,47 +0,0 @@
-{
-	"parser": "babel-eslint",
-	"parserOptions": {
-		"allowImportExportEverywhere": true
-	},
-	"plugins": [
-		"meteor"
-	],
-	"env": {
-		/* Allows global vars from the Meteor environment to pass and enables certain rules */
-		"meteor": true,
-		"node": true,
-		"browser": true
-	},
-	"extends": [
-		"airbnb",
-		"plugin:meteor/recommended"
-	],
-	"settings": {
-		"import/resolver": "meteor"
-	},
-	"rules": {
-		"meteor/no-session": 0, // We are actually using Session for now...
-		"meteor/eventmap-params": [2, {"eventParamName": "event"}],
-		"meteor/eventmap-params": [2, {"templateInstanceParamName": "instance"}],
-		"import/no-extraneous-dependencies": 0,
-		"import/no-unresolved": 0, // There are a bunch of ESLint problems with Meteor's resolver
-		"import/no-duplicates": 0, // So we are disabling these for now
-		"import/extensions": 0,
-		"import/no-absolute-path": 0,
-		"no-console": 0, // For development
-		"no-plusplus": ["error", { "allowForLoopAfterthoughts": true }],
-		"indent": ["error", 4],
-		"new-cap": 0, // Until Match has an exception
-		"func-names": 0, // This is a bit of an annoying rule
-		"no-underscore-dangle": 0, // Doesn't seem to mesh with _id for MongoDB Ids (or SimpleSchema)
-		"max-len": 0, // TODO: re-enable the rules below and fix all of the errors
-		"consistent-return": 0,
-		"no-param-reassign": 0,
-		"no-mixed-operators": 0,
-		"arrow-body-style": 0,
-		"valid-typeof": 0,
-		"import/prefer-default-export": 0
-		"no-undef": 0 
-	},
-	"globals": {}
-}

LesionTracker/.gagarin/.gitignore

@@ -1 +0,0 @@
-local

LesionTracker/.meteor/.finished-upgraders

@@ -1,18 +0,0 @@
-# This file contains information which helps Meteor properly upgrade your
-# app when you run 'meteor update'. You should check it into version control
-# with your project.
-
-notices-for-0.9.0
-notices-for-0.9.1
-0.9.4-platform-file
-notices-for-facebook-graph-api-2
-1.2.0-standard-minifiers-package
-1.2.0-meteor-platform-split
-1.2.0-cordova-changes
-1.2.0-breaking-changes
-1.3.0-split-minifiers-package
-1.3.5-remove-old-dev-bundle-link
-1.4.0-remove-old-dev-bundle-link
-1.4.1-add-shell-server-package
-1.4.3-split-account-service-packages
-1.5-add-dynamic-import-package

LesionTracker/.meteor/.gitignore

@@ -1,2 +0,0 @@
-dev_bundle
-local

LesionTracker/.meteor/.id

@@ -1,7 +0,0 @@
-# This file contains a token that is unique to your project.
-# Check it into your repository along with the rest of this directory.
-# It can be used for purposes such as:
-#   - ensuring you don't accidentally deploy one app on top of another
-#   - providing package authors with aggregated statistics
-
-1q3vtk41m2yk4k1rqj08l

LesionTracker/.meteor/nightwatch.json

@@ -1,136 +0,0 @@
-{
-  "starrynight": {
-    "version": "3.7.0"
-  },
-  "nightwatch": {
-    "version": "0.8.6"
-  },
-  "src_folders": [
-    "./tests/nightwatch/walkthroughs"
-  ],
-  "output_folder": "./tests/nightwatch/reports",
-  "custom_commands_path": [
-    "./tests/nightwatch/commands",
-    "./tests/nightwatch/commands/api/meteor",
-    "./tests/nightwatch/commands/actions",
-    "./tests/nightwatch/commands/components",
-    "./tests/nightwatch/commands/methods"
-  ],
-  "custom_assertions_path": [
-    "./tests/nightwatch/assertions"
-  ],
-  "globals_path": "./tests/nightwatch/globals.json",
-  "selenium": {
-    "start_process": true,
-    "server_path": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/selenium-server-standalone-jar/jar/selenium-server-standalone-2.45.0.jar",
-    "log_path": "tests/nightwatch/logs",
-    "host": "127.0.0.1",
-    "port": 4444,
-    "cli_args": {
-      "webdriver.chrome.driver": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/chromedriver/bin/chromedriver"
-    }
-  },
-  "test_settings": {
-    "default": {
-      "launch_url": "http://localhost:5000",
-      "selenium_host": "127.0.0.1",
-      "selenium_port": 4444,
-      "pathname": "/wd/hub",
-      "silent": true,
-      "disable_colors": false,
-      "firefox_profile": false,
-      "ie_driver": "",
-      "screenshots": {
-        "enabled": false,
-        "path": "./tests/nightwatch/screenshots"
-      },
-      "desiredCapabilities": {
-        "browserName": "chrome",
-        "javascriptEnabled": true,
-        "acceptSslCerts": true,
-        "loggingPrefs": {
-          "browser": "ALL"
-        }
-      },
-      "exclude": "./tests/nightwatch/unittests/*"
-    },
-    "phantomjs": {
-      "desiredCapabilities": {
-        "browserName": "phantomjs",
-        "javascriptEnabled": true,
-        "databaseEnabled": false,
-        "locationContextEnabled": false,
-        "applicationCacheEnabled": false,
-        "browserConnectionEnabled": false,
-        "webStorageEnabled": false,
-        "acceptSslCerts": true,
-        "rotatable": false,
-        "nativeEvents": false,
-        "phantomjs.binary.path": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/phantomjs/bin/phantomjs"
-      }
-    },
-    "travis": {
-      "launch_url": "http://localhost:3000",
-      "selenium_host": "127.0.0.1",
-      "selenium_port": 4444,
-      "pathname": "/wd/hub",
-      "silent": true,
-      "disable_colors": false,
-      "firefox_profile": false,
-      "screenshots": {
-        "enabled": false,
-        "path": "./tests/nightwatch/screenshots"
-      },
-      "desiredCapabilities": {
-        "browserName": "firefox",
-        "javascriptEnabled": true,
-        "databaseEnabled": true,
-        "locationContextEnabled": true,
-        "applicationCacheEnabled": true,
-        "browserConnectionEnabled": true,
-        "webStorageEnabled": true,
-        "acceptSslCerts": true,
-        "rotatable": true,
-        "nativeEvents": true
-      }
-    },
-    "travischrome": {
-      "launch_url": "http://localhost:3000",
-      "selenium_host": "127.0.0.1",
-      "selenium_port": 4444,
-      "pathname": "/wd/hub",
-      "silent": true,
-      "disable_colors": false,
-      "firefox_profile": false,
-      "screenshots": {
-        "enabled": false,
-        "path": "./tests/nightwatch/screenshots"
-      },
-      "desiredCapabilities": {
-        "browserName": "chrome",
-        "javascriptEnabled": true,
-        "databaseEnabled": true,
-        "locationContextEnabled": true,
-        "applicationCacheEnabled": true,
-        "browserConnectionEnabled": true,
-        "webStorageEnabled": true,
-        "acceptSslCerts": true,
-        "rotatable": true,
-        "nativeEvents": true,
-        "chromeOptions": {
-          "args": [
-            "--no-sandbox"
-          ]
-        }
-      }
-    },
-    "unittests": {
-      "selenium": {
-        "start_process": false,
-        "start_session": false
-      },
-      "filter": "./tests/nightwatch/unittests/*",
-      "exclude": ""
-    }
-  }
-}

LesionTracker/.meteor/packages

@@ -1,67 +0,0 @@
-# Meteor packages used by this project, one per line.
-# Check this file (and the other files in this directory) into your repository.
-#
-# 'meteor add' and 'meteor remove' will edit this file for you,
-# but you can also edit it by hand.
-
-npm-bcrypt@0.9.3
-
-meteor-base@1.2.0             # Packages every Meteor app needs to have
-mobile-experience@1.0.5       # Packages for a great mobile UX
-mongo@1.3.0                  # The database Meteor supports right now
-blaze-html-templates@1.0.4    # Compile .html files into Meteor Blaze views
-session@1.1.7                 # Client-side reactive dictionary for your app
-jquery@1.11.10                 # Helpful client-side library
-tracker@1.1.3                 # Meteor's client-side reactive programming library
-standard-minifier-css@1.3.5
-standard-minifier-js@2.2.0
-http@1.3.0
-promise@0.10.0
-stylus@2.513.13
-random@1.0.10
-reactive-var@1.0.11
-reactive-dict@1.2.0
-check@1.2.5
-email@1.2.3
-ecmascript@0.9.0              # Enable ECMAScript2015+ syntax in app code
-
-clinical:active-entry
-clinical:theming
-clinical:fonts
-clinical:hipaa-audit-log
-clinical:hipaa-logger
-
-# OHIF Packages
-ohif:polyfill
-ohif:design
-ohif:core
-ohif:header
-ohif:cornerstone
-ohif:cornerstone-settings
-ohif:viewerbase
-ohif:studies
-ohif:study-list
-ohif:dicom-services
-ohif:hanging-protocols
-ohif:metadata
-
-# Necessary for Lesion Trakcer
-ohif:lesiontracker
-ohif:user
-ohif:user-management
-ohif:select-tree
-
-accounts-base@1.4.0
-accounts-password@1.5.0
-
-twbs:bootstrap
-fortawesome:fontawesome
-momentjs:moment@2.15.1
-aldeed:simple-schema          # Third party package to deal with schemas
-aldeed:template-extension@4.0.0
-aldeed:collection2
-zuuk:stale-session
-dangrossman:bootstrap-daterangepicker
-johdirr:meteor-git-rev
-cultofcoders:persistent-session@0.4.4
-shell-server@0.3.0

LesionTracker/.meteor/platforms

@@ -1,2 +0,0 @@
-server
-browser

LesionTracker/.meteor/release

@@ -1 +0,0 @@
-METEOR@1.6

LesionTracker/.meteor/versions

@@ -1,147 +0,0 @@
-accounts-base@1.4.0
-accounts-password@1.5.0
-aldeed:collection2@2.10.0
-aldeed:collection2-core@1.2.0
-aldeed:schema-deny@1.1.0
-aldeed:schema-index@1.1.1
-aldeed:simple-schema@1.5.3
-aldeed:template-extension@4.1.0
-allow-deny@1.1.0
-amplify@1.0.0
-autoupdate@1.3.12
-babel-compiler@6.24.7
-babel-runtime@1.1.1
-base64@1.0.10
-binary-heap@1.0.10
-blaze@2.3.2
-blaze-html-templates@1.1.2
-blaze-tools@1.0.10
-boilerplate-generator@1.3.0
-caching-compiler@1.1.9
-caching-html-compiler@1.1.2
-callback-hook@1.0.10
-check@1.2.5
-clinical:active-entry@1.5.16
-clinical:auto-resizing@0.2.0
-clinical:fonts@1.1.6
-clinical:hipaa-audit-log@2.4.2
-clinical:hipaa-logger@1.3.0
-clinical:theming@0.4.10
-cultofcoders:persistent-session@0.4.5
-dangrossman:bootstrap-daterangepicker@2.1.13
-ddp@1.4.0
-ddp-client@2.2.0
-ddp-common@1.3.0
-ddp-rate-limiter@1.0.7
-ddp-server@2.1.0
-deps@1.0.12
-diff-sequence@1.0.7
-dynamic-import@0.2.0
-ecmascript@0.9.0
-ecmascript-runtime@0.5.0
-ecmascript-runtime-client@0.5.0
-ecmascript-runtime-server@0.5.0
-ejson@1.1.0
-email@1.2.3
-fastclick@1.0.13
-fortawesome:fontawesome@4.7.0
-geojson-utils@1.0.10
-grove:less@0.2.0
-hot-code-push@1.0.4
-html-tools@1.0.11
-htmljs@1.0.11
-http@1.3.0
-id-map@1.0.9
-iron:controller@1.0.12
-iron:core@1.0.11
-iron:dynamic-template@1.0.12
-iron:layout@1.0.12
-iron:location@1.0.11
-iron:middleware-stack@1.1.0
-iron:router@1.0.13
-iron:url@1.0.11
-johdirr:meteor-git-rev@0.0.4
-jquery@1.11.10
-launch-screen@1.1.1
-livedata@1.0.18
-localstorage@1.2.0
-logging@1.1.19
-mdg:validation-error@0.5.1
-meteor@1.8.0
-meteor-base@1.2.0
-meteor-platform@1.2.6
-minifier-css@1.2.16
-minifier-js@2.2.1
-minimongo@1.4.0
-mobile-experience@1.0.5
-mobile-status-bar@1.0.14
-modules@0.11.0
-modules-runtime@0.9.0
-momentjs:moment@2.19.1
-mongo@1.3.0
-mongo-dev-server@1.1.0
-mongo-id@1.0.6
-mrt:moment@2.8.1
-natestrauser:select2@4.0.3
-npm-bcrypt@0.9.3
-npm-mongo@2.2.33
-observe-sequence@1.0.16
-ohif:commands@0.0.1
-ohif:core@0.0.1
-ohif:cornerstone@0.0.1
-ohif:cornerstone-settings@0.0.1
-ohif:design@0.0.1
-ohif:dicom-services@0.0.1
-ohif:hanging-protocols@0.0.1
-ohif:header@0.0.1
-ohif:hotkeys@0.0.1
-ohif:lesiontracker@0.0.1
-ohif:log@0.0.1
-ohif:measurements@0.0.1
-ohif:metadata@0.0.1
-ohif:polyfill@0.0.1
-ohif:select-tree@0.0.1
-ohif:servers@0.0.1
-ohif:studies@0.0.1
-ohif:study-list@0.0.1
-ohif:themes@0.0.1
-ohif:themes-common@0.0.1
-ohif:user@0.0.1
-ohif:user-management@0.0.1
-ohif:viewerbase@0.0.1
-ohif:wadoproxy@0.0.1
-ordered-dict@1.0.9
-promise@0.10.0
-raix:eventemitter@0.1.3
-random@1.0.10
-rate-limit@1.0.8
-reactive-dict@1.2.0
-reactive-var@1.0.11
-reload@1.1.11
-retry@1.0.9
-routepolicy@1.0.12
-service-configuration@1.0.11
-session@1.1.7
-sha@1.0.9
-shell-server@0.3.0
-silentcicero:jszip@0.0.4
-spacebars@1.0.15
-spacebars-compiler@1.1.3
-srp@1.0.10
-standard-app-packages@1.0.9
-standard-minifier-css@1.3.5
-standard-minifier-js@2.2.1
-stylus@2.513.13
-templating@1.3.2
-templating-compiler@1.3.3
-templating-runtime@1.3.2
-templating-tools@1.1.2
-tracker@1.1.3
-twbs:bootstrap@3.3.6
-ui@1.0.13
-underscore@1.0.10
-url@1.1.0
-validatejs@0.0.1
-webapp@1.4.0
-webapp-hashing@1.0.9
-zuuk:stale-session@1.0.8

LesionTracker/README.md

@@ -1,8 +0,0 @@
-# LesionTracker  
-LesionTracker is an open source, zero-footprint image viewer focused on oncology clinical trial workflows. It is built using Meteor platform which enables modularity with a set of packages of the OHIF framework.  
-
-
-### Why LesionTracker?  
-LesionTracker brings an user experience for the basic tumor metrics through web browser. It provides a DICOM server for storing and streaming images to the viewer, tools for measuring and following lesions over time, and a database for measurements of overlay data. A web-based system for image assessments rather than a workstation-based installed application will improve workflow efficiency, enhance accessibility, and promote collaborative image review for the radiologists at cooperating cancer centers.  
-
-To get started, checkout [LesionTracker Documentation](https://github.com/OHIF/Viewers/wiki/LesionTracker)

LesionTracker/activeEntry.js

@@ -1,46 +0,0 @@
-if (Meteor.isClient){
-    ActiveEntry.configure({
-        logo: {
-            url: '/mini-circles.png',
-            displayed: true
-        },
-        signIn: {
-            displayFullName: true,
-            destination: '/studylist'
-        },
-        signUp: {
-            destination: '/studylist'
-        },
-        themeColors: {
-            primary: ""
-        },
-        passwordOptions: {
-            showPasswordStrengthIndicator: false,
-            requireRegexValidation: true,
-            //requireStrongPasswords: false
-            passwordHistoryCount: 6,
-            failedAttemptsLimit: 5
-        }
-
-    });
-}
-
-/*
-if (Meteor.isServer){
-    Accounts.emailTemplates.siteName = 'AwesomeSite';
-    Accounts.emailTemplates.from = 'AwesomeSite Admin <accounts@example.com>';
-    Accounts.emailTemplates.enrollAccount.subject = function(user) {
-        return 'Welcome to Awesome Town, ' + user.profile.name;
-    };
-
-    Accounts.emailTemplates.enrollAccount.text = function(user, url) {
-        return 'You have been selected to participate in building a better future!'
-            + ' To activate your account, simply click the link below:\n\n'
-            + url;
-    };
-
-    Meteor.startup(function() {
-        //process.env.MAIL_URL = 'smtp://sandboxid.mailgun.org:mypassword@smtp.mailgun.org:587';
-    });
-}
-*/

LesionTracker/bin/medkenOrthanc.bat

@@ -1,2 +0,0 @@
-set METEOR_PACKAGE_DIRS=..\Packages
-meteor --settings ../config/medkenOrthanc.json

LesionTracker/bin/medkenOrthanc.sh

@@ -1 +0,0 @@
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/medkenOrthanc.json

LesionTracker/bin/orthanc.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-declare config='../config/orthancDICOMWeb.json'
-
-if [ $# -gt 0 ]; then
-    if [ "$1" = '--dimse' ]; then
-        config="${config%/*}/orthancDIMSE.json"
-        [ -f "$config" ] && echo "DIMSE config file selected: $config"
-    fi
-fi
-
-echo 'Starting Meteor server...'
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings "$config"

LesionTracker/bin/orthancDICOMWeb.bat

@@ -1,2 +0,0 @@
-set METEOR_PACKAGE_DIRS=..\Packages
-meteor --settings ../config/orthancDICOMWeb.json

LesionTracker/bin/orthancDICOMWeb.sh

@@ -1,2 +0,0 @@
-echo "Starting Meteor server..."
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/orthancDICOMWeb.json

LesionTracker/client/body.html

@@ -1,3 +0,0 @@
-<body>
-    <div id="notificationArea" class="notification-area"></div>
-</body>

LesionTracker/client/body.styl

@@ -1,2 +0,0 @@
-body
-  background-color: black

LesionTracker/client/components/app/app.html

@@ -1,26 +0,0 @@
-<template name="app">
-    {{#header brandHref='http://ohif.org' headerClasses=instance.headerClasses}}
-        {{#section 'brand'}}
-            <svg class="logo-image">
-                <use xlink:href={{absoluteUrl "packages/ohif_viewerbase/assets/icons.svg#icon-ohif-logo"}}></use>
-            </svg>
-            <div class="logo-text">Open Health Imaging Foundation</div>
-        {{/section}}
-        {{#section 'headerAfterBrand'}}
-            {{#if studyListToggleText}}
-                <a href="#" class="btn studyListLinkSection pull-left js-toggle-studyList" id="{{dasherize studyListToggleText}}-btn">
-                    {{studyListToggleText}}
-                </a>
-            {{/if}}
-        {{/section}}
-        {{#section 'headerMenu'}}
-            <span class="user-name pull-left m-r-1">{{userName}}</span>
-            <div class="menu-toggle pull-right">
-                <i class="fa fa-cog"></i>
-                <span class="caret-down"></span>
-            </div>
-        {{/section}}
-    {{/header}}
-
-    {{>Template.dynamic template=(choose this.template 'studylist') data=this}}
-</template>

LesionTracker/client/components/app/app.js

@@ -1,125 +0,0 @@
-import { Template } from 'meteor/templating';
-import { Session } from 'meteor/session';
-import { Router } from 'meteor/iron:router';
-import { ReactiveVar } from 'meteor/reactive-var';
-import { OHIF } from 'meteor/ohif:core';
-
-Template.app.onCreated(() => {
-    const instance = Template.instance();
-    instance.headerClasses = new ReactiveVar('');
-
-    OHIF.header.dropdown.setItems([{
-        action: OHIF.user.audit,
-        text: 'View Audit Log',
-        iconClasses: 'log',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#log',
-        separatorAfter: true
-    }, {
-        action: () => OHIF.ui.showDialog('themeSelectorModal'),
-        text: 'Themes',
-        iconClasses: 'theme',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#theme',
-        separatorAfter: true
-    }, {
-        action: () => OHIF.ui.showDialog('serverInformationModal'),
-        text: 'Server Information',
-        iconClasses: 'server',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#server',
-        separatorAfter: true
-    }, {
-        action: () => OHIF.ui.showDialog('userPreferencesDialog'),
-        text: 'Preferences',
-        icon: 'fa fa-user',
-        separatorAfter: true
-    }, {
-        action: OHIF.user.changePassword,
-        text: 'Change Password',
-        iconClasses: 'password',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#password'
-    }, {
-        action: OHIF.user.logout,
-        text: 'Logout',
-        iconClasses: 'logout',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#logout'
-    }]);
-
-    instance.autorun(() => {
-        const currentRoute = Router.current();
-        if (!currentRoute) return;
-        const routeName = currentRoute.route.getName();
-        const isViewer = routeName.indexOf('viewer') === 0;
-
-        // Add or remove the strech class from body
-        $(document.body)[isViewer ? 'addClass' : 'removeClass']('stretch');
-
-        // Set the header on its bigger version if the viewer is not opened
-        instance.headerClasses.set(isViewer ? '' : 'header-big');
-
-        // Set the viewer open state on session
-        Session.set('ViewerOpened', isViewer);
-    });
-});
-
-Template.app.events({
-    'click .js-toggle-studyList'(event, instance) {
-        event.preventDefault();
-        event.stopPropagation();
-        const isViewer = Session.get('ViewerOpened');
-
-        if (!isViewer) {
-            const timepointId = OHIF.viewer.data.currentTimepointId;
-            if (timepointId) {
-                Router.go('viewerTimepoint', { timepointId });
-            } else {
-                const { studyInstanceUids } = OHIF.viewer.data;
-                Router.go('viewerStudies', { studyInstanceUids });
-            }
-
-            return;
-        }
-
-        OHIF.ui.unsavedChanges.presentProactiveDialog('viewer.*', (hasChanges, userChoice) => {
-            if (!hasChanges) {
-                return Router.go('studylist');
-            }
-
-            switch (userChoice) {
-                case 'abort-action':
-                    return;
-                case 'save-changes':
-                    OHIF.ui.unsavedChanges.trigger('viewer', 'save', false);
-                    OHIF.ui.unsavedChanges.clear('viewer.*');
-                    break;
-                case 'abandon-changes':
-                    OHIF.ui.unsavedChanges.clear('viewer.*');
-                    break;
-            }
-
-            Router.go('studylist');
-        }, {
-            position: {
-                x: event.clientX + 15,
-                y: event.clientY + 15
-            }
-        });
-    }
-});
-
-Template.app.helpers({
-    userName: OHIF.user.getName,
-
-    studyListToggleText() {
-        const isViewer = Session.get('ViewerOpened');
-
-        // Return empty if viewer was not opened yet
-        if (!OHIF.utils.ObjectPath.get(OHIF, 'viewer.data.studyInstanceUids')) return;
-
-        return isViewer ? 'Study list' : 'Back to viewer';
-    },
-
-    dasherize(text) {
-        return text.replace(/ /g, '-').toLowerCase();
-    }
-});
-
-Session.set('defaultSignInMessage', 'Tumor tracking in your browser.');

LesionTracker/client/components/app/app.styl

@@ -1,88 +0,0 @@
-@require "{ohif:design}/app"
-
-body>.header
-
-  .brand
-    height: 30px
-    display: inline-block
-    text-decoration: none
-
-    .logo-image
-      display: inline-block
-      fill: transparent
-      float: left
-      height: 100%
-      margin: 0 8px 0 0
-      width: 30px
-
-    .logo-text
-      display: inline-block
-      font-family: $logoFontFamily
-      font-size: 14px
-      font-weight: $logoFontWeight
-      theme('color', '$textPrimaryColor')
-      line-height: 30px
-
-  .header-menu
-    .user-name
-      font-size: 13px
-
-    .menu-toggle
-      theme('border-left', 'solid 1px $defaultColor')
-      display: inline-block
-      height: 18px
-      padding: 0 8px
-
-      .fa
-        theme('color', '$defaultColor')
-        font-size: 17px
-        line-height: 18px
-
-      .caret-down
-        theme('color', '$uiGrayLight')
-        margin: 0 4px 4px 2px
-
-  .btn
-    theme('color', '$textSecondaryColor')
-    cursor: pointer
-    font-size: 13px
-    font-weight: 500
-    line-height: 26px
-
-    &:hover
-      theme('color', '$hoverColor')
-
-    &:active
-      theme('color', '$activeColor')
-
-  .studyListLinkSection
-    theme('border-left', '%s solid $uiBorderColor' % $uiBorderThickness)
-    margin: 3px 0 0 10px
-    padding: 0 0 0 10px
-
-    &#back-to-viewer-btn
-      border-left: 0
-
-  &.header-big
-    padding-left: $studyListPadding
-    padding-right: $studyListPadding
-
-    .brand
-      height: 100%
-      width: 80%
-      line-height: $topBarExpandedHeight - 10px
-
-      .logo-image
-        margin: 0 20px 0 0
-        width: 50px
-
-      .logo-text
-        font-size: 30px
-
-    .studyListLinkSection
-      border: none
-      left: 0
-      margin: 0
-      padding: 0
-      position: absolute
-      top: 0

LesionTracker/client/components/toolbarSection/toolbarSection.html

@@ -1,37 +0,0 @@
-<template name="toolbarSection">
-    <div class="toolbarSection noselect p-x-2">
-        <div class="clearfix">
-            <div class="pull-left m-t-1">
-                {{>roundedButtonGroup leftSidebarToggleButtonData}}
-            </div>
-
-            {{>toolbarSectionTools toolbarButtons=toolbarButtons}}
-
-            <div class="pull-right m-t-1 rm-x-1">
-                {{#form (extend api=instance.api)}}
-                    {{#button class='btn p-x-2' action='save' disabled=(isFinishDisabled)}}Save{{/button}}
-                {{/form}}
-            </div>
-
-            <div id="toggleMeasurements" class="pull-right m-t-1 rm-x-1">
-                {{>roundedButtonGroup rightSidebarToggleButtonData}}
-            </div>
-            <div id="toggleHUD" class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-3 {{#if session 'measurementTableHudOpen'}}active{{/if}}">
-                <div class="svgContainer">
-                    <svg>
-                        <use xlink:href={{absoluteUrl "packages/ohif_viewerbase/assets/icons.svg#icon-hud"}}></use>
-                    </svg>
-                </div>
-                <div class="buttonLabel">HUD</div>
-            </div>
-            <div id="toggleTrial" class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-1">
-                <div class="svgContainer">
-                    <svg>
-                        <use xlink:href={{absoluteUrl "packages/ohif_viewerbase/assets/icons.svg#icon-trial-info"}}></use>
-                    </svg>
-                </div>
-                <div class="buttonLabel">Trial</div>
-            </div>
-        </div>
-    </div>
-</template>

LesionTracker/client/components/toolbarSection/toolbarSection.js

@@ -1,319 +0,0 @@
-import { Template } from 'meteor/templating';
-import { Session } from 'meteor/session';
-import { Tracker } from 'meteor/tracker';
-import { OHIF } from 'meteor/ohif:core';
-import { Viewerbase } from 'meteor/ohif:viewerbase';
-
-Template.toolbarSection.helpers({
-    isFinishDisabled() {
-        const instance = Template.instance();
-    
-        // Run this computation on save or every time any measurement / timepoint suffer changes
-        OHIF.ui.unsavedChanges.depend();
-        instance.saveObserver.depend();
-        Session.get('LayoutManagerUpdated');
-    
-        return OHIF.ui.unsavedChanges.probe('viewer.*') === 0;
-    },
-
-    leftSidebarToggleButtonData() {
-        const instance = Template.instance();
-        return {
-            toggleable: true,
-            key: 'leftSidebar',
-            value: instance.data.state,
-            options: [{
-                value: 'studies',
-                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-studies',
-                svgWidth: 15,
-                svgHeight: 13,
-                bottomLabel: 'Studies'
-            }]
-        };
-    },
-
-    rightSidebarToggleButtonData() {
-        const instance = Template.instance();
-        return {
-            toggleable: true,
-            key: 'rightSidebar',
-            value: instance.data.state,
-            options: [{
-                value: 'measurements',
-                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-measurements-lesions',
-                svgWidth: 18,
-                svgHeight: 10,
-                bottomLabel: 'Measurements'
-            }]
-        };
-    },
-
-    toolbarButtons() {
-        // Check if the measure tools shall be disabled
-        const isToolDisabled = false; //!Template.instance().data.timepointApi;
-
-        const targetSubTools = [];
-
-        targetSubTools.push({
-            id: 'bidirectional',
-            title: 'Bidirectional',
-            classes: 'imageViewerTool rm-l-3',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-target',
-            disabled: isToolDisabled
-        });
-
-        targetSubTools.push({
-            id: 'targetCR',
-            title: 'CR Target',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-target-cr',
-            disabled: isToolDisabled
-        });
-
-        targetSubTools.push({
-            id: 'targetUN',
-            title: 'UN Target',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-target-un',
-            disabled: isToolDisabled
-        });
-
-        const extraTools = [];
-
-        extraTools.push({
-            id: 'stackScroll',
-            title: 'Stack Scroll',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-stack-scroll'
-        });
-
-        extraTools.push({
-            id: 'resetViewport',
-            title: 'Reset',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-reset'
-        });
-
-        extraTools.push({
-            id: 'rotateR',
-            title: 'Rotate Right',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-rotate-right'
-        });
-
-        extraTools.push({
-            id: 'flipH',
-            title: 'Flip H',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-flip-horizontal'
-        });
-
-        extraTools.push({
-            id: 'flipV',
-            title: 'Flip V',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-flip-vertical'
-        });
-
-        extraTools.push({
-            id: 'invert',
-            title: 'Invert',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-invert'
-        });
-
-        extraTools.push({
-            id: 'magnify',
-            title: 'Magnify',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-magnify'
-        });
-
-        extraTools.push({
-            id: 'ellipticalRoi',
-            title: 'Ellipse',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-elliptical-roi'
-        });
-
-        extraTools.push({
-            id: 'toggleDownloadDialog',
-            title: 'Download',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-camera',
-            active: () => $('#imageDownloadDialog').is(':visible')
-        });
-
-        extraTools.push({
-            id: 'toggleCineDialog',
-            title: 'CINE',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-youtube-play',
-            active: () => $('#cineDialog').is(':visible')
-        });
-
-        const buttonData = [];
-
-        buttonData.push({
-            id: 'zoom',
-            title: 'Zoom',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-zoom'
-        });
-
-        buttonData.push({
-            id: 'wwwc',
-            title: 'Levels',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-levels'
-        });
-
-        buttonData.push({
-            id: 'pan',
-            title: 'Pan',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-pan'
-        });
-
-        buttonData.push({
-            id: 'linkStackScroll',
-            title: 'Link',
-            classes: 'imageViewerCommand toolbarSectionButton nonAutoDisableState',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-link',
-            disableFunction: Viewerbase.viewportUtils.isStackScrollLinkingDisabled
-        });
-
-        buttonData.push({
-            id: 'toggleTarget',
-            title: 'Target',
-            classes: 'rm-l-3',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-target',
-            disabled: isToolDisabled,
-            subTools: targetSubTools
-        });
-
-        buttonData.push({
-            id: 'nonTarget',
-            title: 'Non-Target',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-non-target',
-            disabled: isToolDisabled
-        });
-
-        buttonData.push({
-            id: 'length',
-            title: 'Temp',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp'
-        });
-
-        buttonData.push({
-            id: 'toggleMore',
-            title: 'More',
-            classes: 'rp-x-1 rm-l-3',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-more',
-            disabled: isToolDisabled,
-            subTools: extraTools
-        });
-
-        return buttonData;
-    }
-});
-
-Template.toolbarSection.events({
-    'click #toggleTarget'(event, instance) {
-        const $target = $(event.currentTarget);
-        if (!$target.hasClass('active') && $target.hasClass('expanded')) {
-            Viewerbase.toolManager.setActiveTool('bidirectional');
-        }
-    },
-
-    'click #toggleHUD'(event) {
-        const $this = $(event.currentTarget);
-
-        // Stop here if the tool is disabled
-        if ($this.hasClass('disabled')) {
-            return;
-        }
-
-        const state = Session.get('measurementTableHudOpen');
-        Session.set('measurementTableHudOpen', !state);
-    },
-
-    'click #toggleTrial'(event) {
-        if (!$(event.currentTarget).hasClass('disabled')) {
-            OHIF.ui.showDialog('trialOptionsModal');
-        }
-    }
-});
-
-Template.toolbarSection.onCreated( function() {
-    const instance = Template.instance();
-
-    instance.path = 'viewer.studyViewer.measurements';
-    instance.saveObserver = new Tracker.Dependency();
-    instance.api = {
-        save() {
-            // Clear signaled unsaved changes...
-            const successHandler = () => {
-                OHIF.ui.unsavedChanges.clear(`${instance.path}.*`);
-                instance.saveObserver.changed();
-            };
-    
-            // Display the error messages
-            const errorHandler = data => {
-                OHIF.ui.showDialog('dialogInfo', Object.assign({ class: 'themed' }, data));
-            };
-    
-            const promise = instance.data.measurementApi.storeMeasurements();
-            promise.then(successHandler).catch(errorHandler);
-            OHIF.ui.showDialog('dialogLoading', {
-                promise,
-                text: 'Saving measurement data'
-            });
-    
-            return promise;
-        }
-    };
-
-    instance.unsavedChangesHandler = () => {
-        const isNotDisabled = !instance.$('.js-finish-case').hasClass('disabled');
-        if (isNotDisabled && instance.progressPercent.get() === 100) {
-            instance.api.save();
-        }
-    };
-
-    // Attach handler for unsaved changes dialog...
-    OHIF.ui.unsavedChanges.attachHandler(instance.path, 'save', instance.unsavedChangesHandler);
-});
-
-Template.toolbarSection.onRendered(function() {
-    // Set disabled/enabled tool buttons that are set in toolManager
-    const states = Viewerbase.toolManager.getToolDefaultStates();
-    const disabledToolButtons = states.disabledToolButtons;
-    const allToolbarButtons = $('.toolbarSection').find('.toolbarSectionButton:not(.nonAutoDisableState)');
-
-    // Additional toolbar buttons whose classes are not toolbarSectionButton
-    allToolbarButtons.push($('#toolbarSectionEntry')[0]);
-    allToolbarButtons.push($('#toggleMeasurements')[0]);
-
-    if (disabledToolButtons && disabledToolButtons.length > 0) {
-        for (let i = 0; i < allToolbarButtons.length; i++) {
-            const toolbarButton = allToolbarButtons[i];
-            const index = disabledToolButtons.indexOf($(toolbarButton).attr('id'));
-            if (index !== -1) {
-                $(toolbarButton).addClass('disabled');
-                $(toolbarButton).find('*').addClass('disabled');
-            } else {
-                $(toolbarButton).removeClass('disabled');
-                $(toolbarButton).find('*').removeClass('disabled');
-            }
-        }
-    }
-});
-
-Template.caseProgress.onDestroyed(() => {
-    const instance = Template.instance();
-    // Remove unsaved changes handler after this view has been destroyed...
-    OHIF.ui.unsavedChanges.removeHandler(instance.path, 'save', instance.unsavedChangesHandler);
-});

LesionTracker/client/components/toolbarSection/toolbarSection.styl

@@ -1,27 +0,0 @@
-@import "{ohif:design}/app"
-
-.toolbarSection
-  theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
-  flex: 0 0 auto
-  height: $toolbarHeight
-  padding-top: 6px
-  position: relative
-  transition(height 300ms ease)
-  width: 100%
-
-  &.expanded
-    height: $toolbarHeight + $toolbarDrawerHeight
-
-  .toolbarSectionEntry
-    theme('color', '$defaultColor')
-    cursor: pointer
-    display: inline-block
-    theme('fill', '$defaultColor')
-    margin-top: 3px
-    min-width: 30px
-    theme('stroke', '$defaultColor')
-    text-align: center
-  
-  .saveMeasurements
-    display: inline-block
-    margin-left: 22px

LesionTracker/client/components/viewer/viewer.html

@@ -1,17 +0,0 @@
-<template name="viewer">
-    <div class="viewerDialogs">
-        {{#if and Template.subscriptionsReady dataSourcesReady}}
-            {{>confirmDeleteDialog}}
-            {{>measurementTableHUD (clone this)}}
-            {{>cineDialog}}
-        {{/if}}
-    </div>
-    <div id="viewer">
-        {{#if and Template.subscriptionsReady dataSourcesReady}}
-            {{>toolbarSection (clone this state=state)}}
-            {{>viewerSection (clone this state=state)}}
-        {{else}}
-            {{>loadingText}}
-        {{/if}}
-    </div>
-</template>

LesionTracker/client/components/viewer/viewer.js

@@ -1,388 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { Template } from 'meteor/templating';
-import { Tracker } from 'meteor/tracker';
-import { Session } from 'meteor/session';
-import { ReactiveDict } from 'meteor/reactive-dict';
-import { _ } from 'meteor/underscore';
-import { $ } from 'meteor/jquery';
-import { OHIF } from 'meteor/ohif:core';
-
-import 'meteor/ohif:cornerstone';
-import 'meteor/ohif:viewerbase';
-import 'meteor/ohif:metadata';
-
-Meteor.startup(() => {
-    Session.set('TimepointsReady', false);
-    Session.set('MeasurementsReady', false);
-
-    OHIF.viewer.displaySeriesQuickSwitch = true;
-    OHIF.viewer.stackImagePositionOffsetSynchronizer = new OHIF.viewerbase.StackImagePositionOffsetSynchronizer();
-
-    // Create the synchronizer used to update reference lines
-    OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer('cornerstonenewimage', cornerstoneTools.updateImageSynchronizer);
-
-    OHIF.viewer.metadataProvider = new OHIF.cornerstone.MetadataProvider();
-
-    // Metadata configuration
-    const metadataProvider = OHIF.viewer.metadataProvider;
-    cornerstone.metaData.addProvider(metadataProvider.getProvider());
-
-    // Target tools configuration
-    OHIF.lesiontracker.configureTargetToolsHandles();
-});
-
-Template.viewer.onCreated(() => {
-    Session.set('ViewerReady', false);
-
-    const instance = Template.instance();
-
-    // Define the OHIF.viewer.data global object
-    OHIF.viewer.data = OHIF.viewer.data || Session.get('ViewerData') || {};
-
-    const { TimepointApi, MeasurementApi, ConformanceCriteria } = OHIF.measurements;
-
-    const currentTimepointId = OHIF.viewer.data.currentTimepointId;
-    const timepointApi = new TimepointApi(currentTimepointId);
-    const measurementApi = new MeasurementApi(timepointApi);
-    const conformanceCriteria = new ConformanceCriteria(measurementApi, timepointApi);
-    const apis = {
-        timepointApi,
-        measurementApi,
-        conformanceCriteria
-    };
-
-    Object.assign(OHIF.viewer, apis);
-    Object.assign(instance.data, apis);
-
-    instance.state = new ReactiveDict();
-    instance.state.set('leftSidebar', Session.get('leftSidebar'));
-    instance.state.set('rightSidebar', Session.get('rightSidebar'));
-
-    const viewportUtils = OHIF.viewerbase.viewportUtils;
-
-    OHIF.viewer.functionList = $.extend(OHIF.viewer.functionList, {
-        toggleLesionTrackerTools: OHIF.lesiontracker.toggleLesionTrackerTools,
-        bidirectional: () => {
-            // Used for hotkeys
-            OHIF.viewerbase.toolManager.setActiveTool('bidirectional');
-        },
-        nonTarget: () => {
-            // Used for hotkeys
-            OHIF.viewerbase.toolManager.setActiveTool('nonTarget');
-        },
-        // Viewport functions
-        toggleCineDialog: viewportUtils.toggleCineDialog,
-        clearTools: viewportUtils.clearTools,
-        resetViewport: viewportUtils.resetViewport,
-        invert: viewportUtils.invert,
-        flipV: viewportUtils.flipV,
-        flipH: viewportUtils.flipH,
-        rotateL: viewportUtils.rotateL,
-        rotateR: viewportUtils.rotateR,
-        linkStackScroll: viewportUtils.linkStackScroll
-    });
-
-    if (OHIF.viewer.data.loadedSeriesData) {
-        OHIF.log.info('Reloading previous loadedSeriesData');
-        OHIF.viewer.loadedSeriesData = OHIF.viewer.data.loadedSeriesData;
-    } else {
-        OHIF.log.info('Setting default viewer data');
-        OHIF.viewer.loadedSeriesData = {};
-        OHIF.viewer.data.loadedSeriesData = {};
-    }
-
-    // Store the viewer data in session for further user
-    Session.setPersistent('ViewerData', OHIF.viewer.data);
-
-    Session.set('activeViewport', OHIF.viewer.data.activeViewport || false);
-
-    // Set lesion tool buttons as disabled if pixel spacing is not available for active element
-    instance.autorun(OHIF.lesiontracker.pixelSpacingAutorunCheck);
-
-    // @TypeSafeStudies
-    // Clears OHIF.viewer.Studies collection
-    OHIF.viewer.Studies.removeAll();
-
-    // @TypeSafeStudies
-    // Clears OHIF.viewer.StudyMetadataList collection
-    OHIF.viewer.StudyMetadataList.removeAll();
-
-    instance.data.studies.forEach(study => {
-        const studyMetadata = new OHIF.metadata.StudyMetadata(study, study.studyInstanceUid);
-        let displaySets = study.displaySets;
-
-        if (!study.displaySets) {
-            displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
-            study.displaySets = displaySets;
-        }
-
-        studyMetadata.setDisplaySets(displaySets);
-
-        study.selected = true;
-        OHIF.viewer.Studies.insert(study);
-        OHIF.viewer.StudyMetadataList.insert(studyMetadata);
-    });
-
-    const patientId = instance.data.studies[0].patientId;
-
-    // LT-382: Preventing HP to keep identifying studies in timepoints that might be removed
-    instance.data.studies.forEach(study => (delete study.timepointType));
-
-    // TODO: Consider combining the retrieval calls into one?
-    const timepointsPromise = timepointApi.retrieveTimepoints({ patientId });
-    timepointsPromise.then(() => {
-        const timepoints = timepointApi.all();
-
-        //  Set timepointType in studies to be used in hanging protocol engine
-        timepoints.forEach(timepoint => {
-            timepoint.studyInstanceUids.forEach(studyInstanceUid => {
-                const study = _.find(instance.data.studies, element => {
-                    return element.studyInstanceUid === studyInstanceUid;
-                });
-                if (!study) {
-                    return;
-                }
-
-                // @TODO: Maybe this should be a setCustomAttribute?
-                study.timepointType = timepoint.timepointType;
-            });
-        });
-
-        Session.set('TimepointsReady', true);
-
-        const timepointIds = timepoints.map(t => t.timepointId);
-
-        const measurementsPromise = measurementApi.retrieveMeasurements(patientId, timepointIds);
-        measurementsPromise.then(() => {
-            Session.set('MeasurementsReady', true);
-
-            measurementApi.syncMeasurementsAndToolData();
-        });
-    });
-
-    // Provide the necessary data to the Measurement API and Timepoint API
-    const prior = timepointApi.prior();
-    if (prior) {
-        measurementApi.priorTimepointId = prior.timepointId;
-    }
-
-    //  Enable/Disable Lesion Tracker Tools if the opened study is associated or not
-    OHIF.lesiontracker.toggleLesionTrackerToolsButtons(!!currentTimepointId);
-
-    let firstMeasurementActivated = false;
-    instance.autorun(() => {
-        if (!Session.get('TimepointsReady') ||
-            !Session.get('MeasurementsReady') ||
-            !Session.get('ViewerReady') ||
-            firstMeasurementActivated) {
-            return;
-        }
-
-        // Find and activate the first measurement by Lesion Number
-        // NOTE: This is inefficient, we should be using a hanging protocol
-        // to hang the first measurement's imageId immediately, rather
-        // than changing images after initial loading...
-        const config = OHIF.measurements.MeasurementApi.getConfiguration();
-        const tools = config.measurementTools[0].childTools;
-        const firstTool = tools[Object.keys(tools)[0]];
-        const measurementTypeId = firstTool.id;
-
-        const collection = measurementApi.tools[measurementTypeId];
-        const sorting = {
-            sort: {
-                measurementNumber: -1
-            }
-        };
-
-        const data = collection.find({}, sorting).fetch();
-
-        const current = timepointApi.current();
-        if (!current) {
-            return;
-        }
-
-        let timepoints = [current];
-        const prior = timepointApi.prior();
-        if (prior) {
-            timepoints.push(prior);
-        }
-
-        // TODO: Clean this up, it's probably an inefficient way to get what we need
-        const groupObject = _.groupBy(data, m => m.measurementNumber);
-
-        // Reformat the data
-        const rows = Object.keys(groupObject).map(key => ({
-            measurementTypeId: measurementTypeId,
-            measurementNumber: key,
-            entries: groupObject[key]
-        }));
-
-        const rowItem = rows[0];
-
-        // Activate the first lesion
-        if (rowItem) {
-            OHIF.measurements.jumpToRowItem(rowItem, timepoints);
-        }
-
-        firstMeasurementActivated = true;
-    });
-
-    instance.measurementModifiedHandler = _.throttle((event, instance) => {
-        OHIF.measurements.MeasurementHandlers.onModified(event, instance);
-    }, 300);
-});
-
-/**
- * Sets sidebar configuration and active tool based on viewer template instance
- * @param  {Object} instance Template instance for viewer template
- */
-const setActiveToolAndSidebar = () => {
-    const instance = Template.instance();
-    const { studies, currentTimepointId, measurementApi, timepointIds } = instance.data;
-
-    // Default actions for Associated Studies
-    if (currentTimepointId) {
-        // Follow-up studies: same as the first measurement in the table
-        // Baseline studies: target-tool
-        if (studies[0]) {
-            let activeTool;
-            // In follow-ups, get the baseline timepointId
-            const timepointId = timepointIds.find(id => id !== currentTimepointId);
-
-            // Follow-up studies
-            if (studies[0].timepointType === 'followup' && timepointId) {
-                const measurementTools = OHIF.measurements.MeasurementApi.getConfiguration().measurementTools;
-
-                // Create list of measurement tools
-                const measurementTypes = measurementTools.map(
-                    tool => {
-                        const { id, cornerstoneToolType } = tool;
-                        return {
-                            id,
-                            cornerstoneToolType
-                        };
-                    }
-                );
-
-                // Iterate over each measurement tool to find the first baseline
-                // measurement. If so, stops the loop and prevent fetching from all
-                // collections
-                measurementTypes.every(({ id, cornerstoneToolType }) => {
-                    // Get measurement
-                    if (measurementApi[id]) {
-                        const measurement = measurementApi[id].findOne({ timepointId });
-
-                        // Found a measurement, save tool and stop loop
-                        if (measurement) {
-                            const isArray = Array.isArray(cornerstoneToolType);
-                            activeTool = isArray ? cornerstoneToolType[0] : cornerstoneToolType;
-
-                            return false;
-                        }
-                    }
-
-                    return true;
-                });
-            }
-
-            // If not set, for associated studies default is target-tool
-            OHIF.viewerbase.toolManager.setActiveTool(activeTool || 'bidirectional');
-        }
-
-        // Toggle Measurement Table
-        if (instance.state) {
-            instance.state.set('rightSidebar', 'measurements');
-        }
-    }
-    // Hide as default for single study
-    else {
-        if (instance.state) {
-            instance.state.set('rightSidebar', null);
-        }
-    }
-};
-
-/**
- * Inits OHIF Hanging Protocol's onReady.
- * It waits for OHIF Hanging Protocol to be ready to instantiate the ProtocolEngine
- * Hanging Protocol will use OHIF LayoutManager to render viewports properly
- */
-
-const initHangingProtocol = () => {
-    // When Hanging Protocol is ready
-    HP.ProtocolStore.onReady(() => {
-
-        setActiveToolAndSidebar();
-
-        // Gets all StudyMetadata objects: necessary for Hanging Protocol to access study metadata
-        const studyMetadataList = OHIF.viewer.StudyMetadataList.all();
-
-        // Caches Layout Manager: Hanging Protocol uses it for layout management according to current protocol
-        const layoutManager = OHIF.viewerbase.layoutManager;
-
-        // Instantiate StudyMetadataSource: necessary for Hanging Protocol to get study metadata
-        const studyMetadataSource = new OHIF.studies.classes.OHIFStudyMetadataSource();
-
-        // Creates Protocol Engine object with required arguments
-        const ProtocolEngine = new HP.ProtocolEngine(layoutManager, studyMetadataList, [], studyMetadataSource);
-
-        // Sets up Hanging Protocol engine
-        HP.setEngine(ProtocolEngine);
-
-        Session.set('ViewerReady', true);
-
-        Session.set('activeViewport', 0);
-    });
-};
-
-Template.viewer.onRendered(function() {
-    this.autorun(() => {
-        // To make sure ohif viewerMain is rendered before initializing Hanging Protocols
-        const isOHIFViewerMainRendered = Session.get('OHIFViewerMainRendered');
-
-        // To avoid first run
-        if (isOHIFViewerMainRendered) {
-            // To run only when ViewerMainRendered dependency has changed.
-            // because initHangingProtocol can have other reactive components
-            Tracker.nonreactive(initHangingProtocol);
-        }
-    });
-});
-
-Template.viewer.helpers({
-    dataSourcesReady() {
-        // TODO: Find a better way to do this
-        const ready = Session.get('TimepointsReady') && Session.get('MeasurementsReady');
-        OHIF.log.info('dataSourcesReady? : ' + ready);
-        return ready;
-    },
-
-    state() {
-        return Template.instance().state;
-    }
-});
-
-Template.viewer.events({
-    'cornerstonetoolsmeasurementadded .imageViewerViewport'(event, instance) {
-        const originalEvent = event.originalEvent;
-        OHIF.measurements.MeasurementHandlers.onAdded(originalEvent, instance);
-    },
-
-    'cornerstonetoolsmeasurementmodified .imageViewerViewport'(event, instance) {
-        const originalEvent = event.originalEvent;
-        instance.measurementModifiedHandler(originalEvent, instance);
-    },
-
-    'cornerstonemeasurementremoved .imageViewerViewport'(event, instance) {
-        const originalEvent = event.originalEvent;
-        OHIF.measurements.MeasurementHandlers.onRemoved(originalEvent, instance);
-    }
-});
-
-Template.viewer.onDestroyed(() => {
-    Session.set('ViewerMainReady', false);
-    Session.set('TimepointsReady', false);
-    Session.set('MeasurementsReady', false);
-
-    OHIF.viewer.stackImagePositionOffsetSynchronizer.deactivate();
-});

LesionTracker/client/components/viewer/viewer.styl

@@ -1,55 +0,0 @@
-@import "{ohif:design}/app"
-
-#viewer
-  background-color: black
-  height: 100%
-  width: 100%
-
-#imageViewerViewports
-  .viewportContainer
-    border: none !important
-    outline: 0 !important // Prevent blue outline in Chrome
-    position: relative
-
-    &:hover
-    &.active
-    &:hover.active
-      border: none !important
-      outline: 0 !important // Prevent blue outline in Chrome
-
-    .removable
-      .imageViewerViewport
-        theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
-
-        canvas
-          border-color: transparent
-          border-style: solid
-          border-width: 1px
-
-    &:not(:last-child)
-    .removable
-      .imageViewerViewport
-        theme('border-right', '%s solid $uiBorderColor' % $uiBorderThickness)
-
-    &:first-child
-      .removable
-        .imageViewerViewport
-          theme('border-left', '%s solid $uiBorderColor' % $uiBorderThickness)
-
-    &.active
-      .removable
-        .imageViewerViewport
-          border-right: none !important
-
-          canvas
-            theme('border-color', '$uiBorderColorActive')
-
-
-.sidebar-left-open
-  #layoutManagerTarget
-    #imageViewerViewports
-      .viewportContainer
-        &:first-child
-          .removable
-            .imageViewerViewport
-              border-left: none

LesionTracker/client/components/viewerSection/viewerSection.html

@@ -1,21 +0,0 @@
-<template name="viewerSection">
-    <div class="viewerSection">
-        <div class="sidebarMenu sidebar-left {{#if leftSidebarOpen}}sidebar-open{{/if}}">
-            {{#if isTimepointBrowser}}
-                {{>timepointBrowserSidebar (clone this)}}
-            {{else}}
-                {{#if instance.loading.get}}
-                    {{>loadingText}}
-                {{else}}
-                    {{>studyBrowserSidebar (clone this studiesInformation=instance.studiesInformation.get)}}
-                {{/if}}
-            {{/if}}
-        </div>
-        <div class="mainContent {{#if leftSidebarOpen}}sidebar-left-open{{/if}} {{#if rightSidebarOpen}}sidebar-right-open{{/if}}">
-            {{>viewerMain (clone this)}}
-        </div>
-        <div class="sidebarMenu sidebar-right {{#if rightSidebarOpen}}sidebar-open{{/if}}">
-            {{>measurementTable (clone this)}}
-        </div>
-    </div>
-</template>

LesionTracker/client/components/viewerSection/viewerSection.js

@@ -1,72 +0,0 @@
-import { Template } from 'meteor/templating';
-import { ReactiveVar } from 'meteor/reactive-var';
-import { $ } from 'meteor/jquery';
-import { OHIF } from 'meteor/ohif:core';
-
-Template.viewerSection.onCreated(() => {
-    const instance = Template.instance();
-
-    instance.isTimepointBrowser = () => !!OHIF.viewer.data.currentTimepointId;
-
-    OHIF.viewer.quickSwitchStudyBrowserTemplate = 'timepointBrowserQuickSwitch';
-    if (!instance.isTimepointBrowser()) {
-        OHIF.viewer.quickSwitchStudyBrowserTemplate = 'studyBrowserQuickSwitch';
-        instance.loading = new ReactiveVar(true);
-        instance.studiesInformation = new ReactiveVar([]);
-        const filter = { studyInstanceUid: OHIF.viewer.data.studyInstanceUids };
-        OHIF.studies.searchStudies(filter).then(studiesData => {
-            instance.loading.set(false);
-            instance.studiesInformation.set(studiesData);
-        }).catch(error => {
-            instance.loading.set(false);
-            const text = 'An error has occurred while retrieving studies information';
-            OHIF.ui.notifications.danger({ text });
-            OHIF.log.error(error);
-        });
-    }
-});
-
-Template.viewerSection.events({
-    'transitionend .sidebarMenu'(event) {
-        if (!event.target.classList.contains('sidebarMenu')) return;
-        window.ResizeViewportManager.handleResize();
-    },
-
-    'ohif.lesiontracker.timepoint.changeViewType .timepoint-browser-list'(event, instance, viewType) {
-        const $browserList = $(event.currentTarget);
-        const $allBrowserItems = $browserList.find('.timepoint-browser-item');
-
-        // Removes all active classes to collapse the timepoints and studies
-        $allBrowserItems.removeClass('active');
-
-        if (viewType === 'key') {
-            const { timepointIds, currentTimepointId } = OHIF.viewer.data;
-            timepointIds.forEach(timepointId => {
-                const $browserItem = $allBrowserItems.filter(`[data-id=${timepointId}]`);
-                $browserItem.find('.timepoint-item').trigger('ohif.lesiontracker.timepoint.load');
-            });
-
-            // Show only current timepoint expanded on key timepoints tab
-            const $browserItem = $allBrowserItems.filter(`[data-id=${currentTimepointId}]`);
-            $browserItem.find('.timepoint-item').trigger('click');
-        }
-    }
-});
-
-Template.viewerSection.helpers({
-    leftSidebarOpen() {
-        return Template.instance().data.state.get('leftSidebar');
-    },
-
-    rightSidebarOpen() {
-        return Template.instance().data.state.get('rightSidebar');
-    },
-
-    isTimepointBrowser() {
-        return Template.instance().isTimepointBrowser();
-    },
-
-    studiesInformation() {
-        return Template.instance().studiesInformation.get();
-    }
-});

LesionTracker/client/components/viewerSection/viewerSection.styl

@@ -1,81 +0,0 @@
-@require '{ohif:design}/app'
-
-.viewerSection
-  display: flex
-  flex: 1
-  flex-flow: row nowrap
-  align-items: stretch
-  height: 'calc(100% - %s)' % ($toolbarHeight + $topBarHeight)
-  width: 100%
-
-  .sidebarMenu
-    height: 100%
-    // required transformation to make inner fixed elements relative to this one
-    transform(scale(1))
-    transition($sidebarTransition)
-
-    .sidebar-option
-      height: 100%
-      max-width: inherit
-      position: absolute
-      transform(translateX(100%))
-      transition($sidebarTransition)
-      width: 100%
-
-      &.active
-        transform(translateX(0%))
-
-  .sidebar-left
-    theme('border-right', '%s solid $uiBorderColor' % $uiBorderThickness)
-    flex: 1
-    margin-left: - $studiesSidebarMenuWidth
-    max-width: $studiesSidebarMenuWidth
-    order: 1
-    visibility: hidden
-
-    &.sidebar-open
-      margin-left: 0
-      visibility: visible
-
-  .loadingTextDiv
-    theme('color', '$textSecondaryColor')
-    font-size: 32px
-
-  .mainContent
-    flex: 1
-    height: 100%
-    order: 2
-    overflow: visible
-    position: relative
-    transition($sidebarTransition)
-    width: 100%
-
-    .viewerMain
-      left: 0
-      position: absolute
-      top: 0
-
-  .sidebar-right
-    flex: 1
-    margin-right: - $lesionsSidebarMenuWidth
-    max-width: $lesionsSidebarMenuWidth
-    order: 3
-    position: relative
-    visibility: hidden
-
-    &[data-timepoints="3"]
-      margin-right: - ($lesionsSidebarMenuWidth + 135.5px)
-      max-width: $lesionsSidebarMenuWidth + 135.5px
-
-    &[data-timepoints="4"]
-      margin-right: - ($lesionsSidebarMenuWidth + 270px)
-      max-width: $lesionsSidebarMenuWidth + 270px
-
-    &.sidebar-open
-      margin-right: 0
-      visibility: visible
-
-  .studiesListedChanger
-    theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
-    padding: 20px 10px
-    text-align: center

LesionTracker/client/config.js

@@ -1,34 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { Accounts } from 'meteor/accounts-base';
-import { OHIF } from 'meteor/ohif:core';
-import { cornerstoneWADOImageLoader } from 'meteor/ohif:cornerstone';
-
-Meteor.startup(function() {
-	const maxWebWorkers = Math.max(navigator.hardwareConcurrency - 1, 1);
-    const config = {
-	    maxWebWorkers: maxWebWorkers,	
-    	startWebWorkersOnDemand: true,
-        webWorkerPath : OHIF.utils.absoluteUrl('packages/ohif_cornerstone/public/js/cornerstoneWADOImageLoaderWebWorker.es5.js'),
-        taskConfiguration: {
-            'decodeTask' : {
-		        loadCodecsOnStartup : true,
-		        initializeCodecsOnStartup: false,
-                codecsPath: OHIF.utils.absoluteUrl('packages/ohif_cornerstone/public/js/cornerstoneWADOImageLoaderCodecs.es5.js'),
-                usePDFJS: false
-            }
-        }
-    };
-
-    cornerstoneWADOImageLoader.webWorkerManager.initialize(config);
-
-    cornerstoneWADOImageLoader.configure({
-        beforeSend: function(xhr) {
-            const userId = Meteor.userId();
-            const loginToken = Accounts._storedLoginToken();
-            if (userId && loginToken) {
-                xhr.setRequestHeader("x-user-id", userId);
-                xhr.setRequestHeader("x-auth-token", loginToken);
-            }
-        }
-    });
-});

LesionTracker/client/head.html

@@ -1,17 +0,0 @@
-<head>
-    <meta charset="utf-8">
-    <title>Lesion Tracker</title>
-    <meta name="description" content="Prototype viewer application for oncology">
-    <!-- Prevents page zooming -->
-    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no">
-
-    <link rel="shortcut icon" type="image/png" href="/images/logo.png" sizes="16x16 32x32 64x64">
-    <!--Best display for mobile devices-->
-    <meta http-equiv="cleartype" content="on">
-    <meta name="MobileOptimized" content="320">
-    <meta name="HandheldFriendly" content="True">
-    <meta name="apple-mobile-web-app-capable" content="yes">
-
-    <!-- Make SVG work on IE -->
-    <meta http-equiv="X-UA-Compatible" content="IE=edge">
-</head>

LesionTracker/client/lesionTrackerHangingProtocol.js

@@ -1,111 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-
-Meteor.startup(() => {
-    console.log('Adding Lesion Tracker Hanging Protocols');
-
-    //------------------------------------------------------------------------------
-    // Define Baseline protocol
-    const proto = new HP.Protocol('LT_Baseline');
-    proto.locked = true;
-
-    const isBaseline = new HP.ProtocolMatchingRule();
-    isBaseline.required = true;
-    isBaseline.weight = 1;
-    isBaseline.attribute = 'timepointType';
-    isBaseline.constraint = {
-        equals: {
-            value: 'baseline'
-        }
-    };
-
-    proto.addProtocolMatchingRule(isBaseline);
-
-    const oneByOne = new HP.ViewportStructure('grid', {
-        rows: 1,
-        columns: 1
-    });
-
-    // Stage 1
-    const single = new HP.Viewport();
-
-    const baseline = new HP.StudyMatchingRule(true);
-    baseline.required = true;
-    baseline.attribute = 'timepointType';
-    baseline.constraint = {
-        equals: {
-            value: 'baseline'
-        }
-    };
-
-    single.studyMatchingRules.push(baseline);
-
-    const first = new HP.Stage(oneByOne, 'oneByOne');
-    first.viewports.push(single);
-
-    proto.addStage(first);
-
-    HP.lesionTrackerBaselineProtocol = proto;
-    HP.lesionTrackerBaselineProtocol.id = 'lesionTrackerBaselineProtocol';
-
-    //------------------------------------------------------------------------------
-    // Define Followup Protocol
-    const protoFollowup = new HP.Protocol('LT_BaselineFollowup');
-    protoFollowup.locked = true;
-
-    const isFollowup = new HP.ProtocolMatchingRule();
-    isFollowup.required = true;
-    isFollowup.weight = 2;
-    isFollowup.attribute = 'timepointType';
-    isFollowup.constraint = {
-        equals: {
-            value: 'followup'
-        }
-    };
-
-    protoFollowup.addProtocolMatchingRule(isFollowup);
-
-    const oneByTwo = new HP.ViewportStructure('grid', {
-        rows: 1,
-        columns: 2
-    });
-
-    // Stage 1
-    const left = new HP.Viewport();
-    const right = new HP.Viewport();
-
-    const baseline2 = new HP.StudyMatchingRule(true);
-    baseline2.required = true;
-    baseline2.attribute = 'timepointType';
-    baseline2.constraint = {
-        equals: {
-            value: 'baseline'
-        }
-    };
-
-    const followup = new HP.StudyMatchingRule();
-    followup.required = true;
-    followup.attribute = 'timepointType';
-    followup.constraint = {
-        equals: {
-            value: 'followup'
-        }
-    };
-
-    left.studyMatchingRules.push(followup);
-    right.studyMatchingRules.push(baseline2);
-
-    const first2 = new HP.Stage(oneByTwo, 'oneByTwo');
-    first2.viewports.push(left);
-    first2.viewports.push(right);
-
-    protoFollowup.addStage(first2);
-
-    HP.lesionTrackerFollowupProtocol = protoFollowup;
-    HP.lesionTrackerFollowupProtocol.id = 'lesionTrackerFollowupProtocol';
-
-    HP.ProtocolStore.onReady(() => {
-        console.log('Inserting lesion tracker protocols');
-        HP.ProtocolStore.addProtocol(HP.lesionTrackerBaselineProtocol);
-        HP.ProtocolStore.addProtocol(HP.lesionTrackerFollowupProtocol);
-    });
-});

LesionTracker/client/lib/customCommands.js

@@ -1,53 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { _ } from 'meteor/underscore';
-import { OHIF } from 'meteor/ohif:core';
-
-Meteor.startup(() => {
-    const { toolManager } = OHIF.viewerbase;
-    const contextName = 'viewer';
-
-    // Enable the custom tools
-    const customTools = [{
-        id: 'bidirectional',
-        name: 'Target'
-    }, {
-        id: 'nonTarget',
-        name: 'Non-Target'
-    }, {
-        id: 'targetCR',
-        name: 'CR Target'
-    }, {
-        id: 'targetUN',
-        name: 'UN Target'
-    }];
-    customTools.forEach(tool => {
-        _.defaults(OHIF.hotkeys.defaults[contextName], { [tool.id]: '' });
-        OHIF.commands.register(contextName, tool.id, {
-            name: tool.name,
-            action: tool.action || (() => toolManager.setActiveTool(tool.id))
-        });
-    });
-
-    // Enable the custom commands
-    const customCommands = [{
-        id: 'linkStackScroll',
-        name: 'Link',
-        action: OHIF.viewerbase.viewportUtils.linkStackScroll
-    }, {
-        id: 'saveMeasurements',
-        name: 'Save measurements',
-        hotkey: 'CTRL+S',
-        action() {
-            const activeTimepoint = OHIF.measurements.getActiveTimepoint();
-            if (!activeTimepoint) return;
-            OHIF.measurements.saveMeasurements(OHIF.viewer.measurementApi, activeTimepoint.timepointId);
-        }
-    }];
-    customCommands.forEach(command => {
-        _.defaults(OHIF.hotkeys.defaults[contextName], { [command.id]: command.hotkey || '' });
-        OHIF.commands.register(contextName, command.id, {
-            name: command.name,
-            action: command.action || (() => toolManager.setActiveTool(command.id))
-        });
-    });
-});

LesionTracker/client/log.js

@@ -1,3 +0,0 @@
-import loglevel from 'loglevel';
-log = loglevel.getLogger('OHIFViewer');
-log.setLevel('info');

LesionTracker/client/routes.js

@@ -1,62 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { Router } from 'meteor/iron:router';
-import { OHIF } from 'meteor/ohif:core';
-
-Router.configure({
-    layoutTemplate: 'layout',
-    loadingTemplate: 'layout'
-});
-
-Router.onBeforeAction('loading');
-
-Router.onBeforeAction(function() {
-    // verifyEmail controls whether emailVerification template will be rendered or not
-    const publicSettings = Meteor.settings && Meteor.settings.public;
-    const verifyEmail = publicSettings && publicSettings.verifyEmail || false;
-
-    // Check if user is signed in or needs an email verification
-    if (!Meteor.userId() && !Meteor.loggingIn()) {
-        this.render('entrySignIn');
-    } else if (verifyEmail && Meteor.user().emails && !Meteor.user().emails[0].verified) {
-        this.render('emailVerification');
-    } else {
-        this.next();
-    }
-}, {
-    except: ['entrySignIn', 'entrySignUp', 'forgotPassword', 'resetPassword', 'emailVerification']
-});
-
-Router.route('/', function() {
-    Router.go('studylist', {}, { replaceState: true });
-}, { name: 'home' });
-
-Router.route('/studylist', {
-    name: 'studylist',
-    onBeforeAction: function() {
-        const next = this.next;
-
-        // Retrieve the timepoints data to display in studylist
-        const promise = OHIF.studylist.timepointApi.retrieveTimepoints({});
-        promise.then(() => next());
-    },
-    action: function() {
-        this.render('app', { data: { template: 'studylist' } });
-    }
-});
-
-Router.route('/viewer/timepoints/:timepointId', function() {
-    const timepointId = this.params.timepointId;
-    OHIF.viewerbase.renderViewer(this, { timepointId });
-}, { name: 'viewerTimepoint' });
-
-Router.route('/viewer/studies/:studyInstanceUids', function() {
-    const studyInstanceUids = this.params.studyInstanceUids.split(';');
-    OHIF.viewerbase.renderViewer(this, { studyInstanceUids });
-}, { name: 'viewerStudies' });
-
-// OHIF #98 Show specific series of study
-Router.route('/study/:studyInstanceUid/series/:seriesInstanceUids', function () {
-    const studyInstanceUid = this.params.studyInstanceUid;
-    const seriesInstanceUids = this.params.seriesInstanceUids.split(';');
-    OHIF.viewerbase.renderViewer(this, { studyInstanceUids: [studyInstanceUid], seriesInstanceUids });
-}, { name: 'viewerSeries' });

LesionTracker/package.json

@@ -1,38 +0,0 @@
-{
-  "name": "LesionTracker",
-  "private": true,
-  "scripts": {
-    "lint": "eslint .",
-    "fix": "eslint --fix .",
-    "pretest": "npm run lint --silent"
-  },
-  "version": "1.0.0",
-  "description": "",
-  "dependencies": {
-    "babel-runtime": "^6.23.0",
-    "bcrypt": "^0.8.7",
-    "loglevel": "^1.4.1",
-    "meteor-node-stubs": "^0.2.3"
-  },
-  "devDependencies": {
-    "babel-eslint": "^6.1.2",
-    "eslint": "^3.7.0",
-    "eslint-config-airbnb": "^12.0.0",
-    "eslint-import-resolver-meteor": "^0.3.3",
-    "eslint-plugin-import": "^1.16.0",
-    "eslint-plugin-jsx-a11y": "^2.2.2",
-    "eslint-plugin-meteor": "^4.0.0",
-    "eslint-plugin-react": "^6.3.0"
-  },
-  "main": "index.js",
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/OHIF/Viewers.git"
-  },
-  "author": "OHIF",
-  "license": "MIT",
-  "bugs": {
-    "url": "https://github.com/OHIF/Viewers/issues"
-  },
-  "homepage": "https://github.com/OHIF/Viewers"
-}

LesionTracker/runGagarinTests.sh

@@ -1 +0,0 @@
-starrynight run-tests --framework gagarin --debug --verbose --webdriver http://localhost:9515 --path ../Packages/*/tests/gagarin/**/*.js

LesionTracker/runNightwatchTests.sh

@@ -1 +0,0 @@
-starrynight run-tests --framework nightwatch

LesionTracker/server/email.js

@@ -1,52 +0,0 @@
-import { OHIF } from 'meteor/ohif:core';
-
-Meteor.startup(function () {
-
-    // Mail server settings
-    var username = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.username || null;
-    var password = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.password || null;
-    var server = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.server || null;
-    var port = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.port || null;
-    var verifyEmail = Meteor.settings && Meteor.settings.public && Meteor.settings.public.verifyEmail || false;
-    var siteName = Meteor.settings && Meteor.settings.public && Meteor.settings.public.siteName || "Lesion Tracker";
-
-    if (username && password && server && port) {
-        Accounts.emailTemplates.siteName = siteName;
-        Accounts.emailTemplates.from = siteName+' Admin <'+username+'>';
-
-        process.env.MAIL_URL = 'smtp://' +
-            encodeURIComponent(username) + ':' +
-            encodeURIComponent(password) + '@' +
-            encodeURIComponent(server) + ':' + port;
-
-        // Subject line of the email.
-        Accounts.emailTemplates.verifyEmail.subject = function(user) {
-            return 'Confirm Your Email Address for '+siteName;
-        };
-
-        // Email text
-        Accounts.emailTemplates.verifyEmail.text = function(user, url) {
-            return 'Thank you for registering.  Please click on the following link to verify your email address: \r\n' + url;
-        };
-
-        // Reset password mail
-        Accounts.emailTemplates.resetPassword.subject = function() {
-          return 'Reset your '+siteName+' password'
-        };
-
-        Accounts.urls.resetPassword = function(token) {
-            return OHIF.utils.absoluteUrl('resetPassword/' + token);
-        };
-
-        Accounts.emailTemplates.resetPassword.text = function(user, url) {
-            return "Hello " + user.profile.fullName + ",\n\n" +
-                "Click the following link to set your new password:\n" +
-                url + "\n\n";
-        };
-
-        // Send email when account is created
-        Accounts.config({
-            sendVerificationEmail: verifyEmail
-        });
-    }
-});

LesionTracker/tests/nightwatch/.npmignore

@@ -1 +0,0 @@
-reports

LesionTracker/tests/nightwatch/assertions/sampleAssertion.js

@@ -1,4 +0,0 @@
-exports.assertion = function() {
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/actions/sampleAction.js

@@ -1,4 +0,0 @@
-exports.command = function() {
-
-    return this;
-};

LesionTracker/tests/nightwatch/commands/api/entry/reviewSignInPage.js

@@ -1,15 +0,0 @@
-exports.command = function(username, password) {
-  this
-    .waitForElementVisible('#entrySignIn', 1000)
-      .verify.elementPresent("#signInPageTitle")
-      .verify.elementPresent("#signInPageMessage")
-      .verify.elementPresent("#signInPageEmailInput")
-      .verify.elementPresent("#signInPagePasswordInput")
-      .verify.elementPresent("#signInToAppButton")
-      .verify.elementPresent("#needAnAccountButton")
-
-      .verify.containsText("#signInPageTitle", "Sign In")
-      .verify.containsText("#signInPageMessage", "Improve your clincal practice with checklists.")
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/api/entry/reviewSignUpPage.js

@@ -1,11 +0,0 @@
-exports.command = function(username, password) {
-  this
-    .waitForElementVisible('#entrySignUp', 1000)
-      .verify.elementPresent("#signUpPageEmailInput")
-      .verify.elementPresent("#signUpPagePasswordInput")
-      .verify.elementPresent("#signUpPagePasswordConfirmInput")
-
-      .verify.elementPresent("#signUpPageJoinNowButton")
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/api/entry/signIn.js

@@ -1,14 +0,0 @@
-exports.command = function(username, password) {
-
-  this
-    .waitForElementVisible('#entrySignIn', 1000)
-      .verify.elementPresent("#signInPageEmailInput")
-      .verify.elementPresent("#signInPagePasswordInput")
-
-      .setValue("#signInPageEmailInput", username)
-      .setValue("#signInPagePasswordInput", password)
-
-    .click("#signInToAppButton").pause(1000)
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/api/entry/signOut.js

@@ -1,8 +0,0 @@
-exports.command = function(email, password) {
-
-  this
-    .verify.elementPresent("#logoutButton")
-    .click("#logoutButton").pause(500)
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/api/entry/signUp.js

@@ -1,23 +0,0 @@
-exports.command = function(email, password) {
-
-  this
-    .waitForElementVisible('#entrySignUp', 1000)
-      .verify.elementPresent("#signUpPageEmailInput")
-      .verify.elementPresent("#signUpPagePasswordInput")
-      .verify.elementPresent("#signUpPagePasswordConfirmInput")
-
-      .clearValue("#signUpPageEmailInput")
-      .clearValue("#signUpPagePasswordInput")
-      .clearValue("#signUpPagePasswordConfirmInput")
-
-      // .setValue("#signUpPageUsernameInput", "Jane Doe")
-      .setValue("#signUpPageEmailInput", email)
-      .setValue("#signUpPagePasswordInput", password)
-      .setValue("#signUpPagePasswordConfirmInput", password)
-
-      .click("#signUpPageJoinNowButton").pause(200)
-
-
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/api/meteor/callMeteorMethod.js

@@ -1,21 +0,0 @@
-// async version calls method on the server
-exports.command = function(methodName, timeout) {
-  var client = this;
-  if (!timeout) {
-      timeout = 5000;
-  }
-
-  this
-    .timeoutsAsyncScript(timeout)
-    .executeAsync(function(data, meteorCallback){
-      //return HipaaLogger.logEventObject(data);
-      Meteor.call(methodName, data, function(meteorError, meteorResult){
-        var response = (meteorError ? { error: meteorError } : { result: meteorResult });
-        meteorCallback(response);
-      })
-    }, [hipaaEvent], function(result){
-      console.log("result.value", result.value);
-      client.assert.ok(result.value);
-    }).pause(1000)
-    return this;
-};

LesionTracker/tests/nightwatch/commands/api/meteor/checkSession.js

@@ -1,40 +0,0 @@
-/*exports.command = function(sessionName, expectedValue, timeout, callback) {
-
-    var self = this;
-    if (!timeout) {
-        timeout = 5000;
-    }
-
-    var glassOpacity = false;
-
-    this
-      .timeoutsAsyncScript(timeout)
-        .executeAsync(function (data, callback) {
-            return Session.get('glassOpacity');
-        }, [''], function (response) { // you need to pass an ARRAY of ONE argument, must be a bug
-            if (response.value.error) {
-                throw 'Meteor apply (call) returned an error: ' + response.value.error;
-            } else if (typeof callback === 'function') {
-              callback.call(self);
-            }
-        })
-    return this;
-};*/
-
-
-
-
-// syncrhonous version; only works for checking javascript objects on client
-exports.command = function(sessionVarName, expectedValue) {
-  var client = this;
-  this
-    .execute(function(data){
-      return Session.get(data);
-    }, [sessionVarName], function(result){
-      client.assert.ok(result.value);
-      if(expectedValue){
-        client.assert.equal(result.value, expectedValue);
-      }
-    }).pause(1000)
-    return this;
-};

LesionTracker/tests/nightwatch/commands/components/reviewMainLayout.js

@@ -1,10 +0,0 @@
-exports.command = function(username, password) {
-  this
-    .verify.elementPresent("#appBody")
-      .verify.elementPresent("#navbarHeader")
-        .verify.elementPresent("#contentContainer")
-        .verify.elementPresent("#contentContainer .content-scrollable")
-      .verify.elementPresent("#navbarFooter")
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/methods/objectMethod.js

@@ -1,22 +0,0 @@
-// async version calls method on the server
-exports.command = function(methodName, timeout) {
-  /*var client = this;
-  if (!timeout) {
-      timeout = 5000;
-  }
-
-  this
-    .timeoutsAsyncScript(timeout)
-    .executeAsync(function(data, meteorCallback){
-      //return HipaaLogger.logEventObject(data);
-      Meteor.call(methodName, data, function(meteorError, meteorResult){
-        var response = (meteorError ? { error: meteorError } : { result: meteorResult });
-        meteorCallback(response);
-      })
-    }, [hipaaEvent], function(result){
-      console.log("result.value", result.value);
-      client.assert.ok(result.value);
-    }).pause(1000)
-    return this;*/
-    return this;
-};

LesionTracker/tests/nightwatch/commands/sectionBreak.js

@@ -1,9 +0,0 @@
-exports.command = function(input, callback) {
-
-  this
-    .frame(null)
-    .waitForElementVisible("body", 1000, "=============================================================")
-    .verify.elementPresent("body", "== " + input)
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/commands/waitForPage.js

@@ -1,7 +0,0 @@
-exports.command = function(pageId) {
-
-  this
-    .waitForElementVisible(pageId, 3000)
-
-  return this; // allows the command to be chained.
-};

LesionTracker/tests/nightwatch/globals.json

@@ -1,8 +0,0 @@
-{
-  "default" : {
-    "myGlobal" : 1
-  },
-  "test_env" : {
-    "myGlobal" : 2
-  }
-}

LesionTracker/tests/nightwatch/logs/selenium-debug.log

@@ -1 +0,0 @@
-hh:mm:ss.sss INFO - Initializing debug log

LesionTracker/tests/nightwatch/unittests/foo.js

@@ -1,34 +0,0 @@
-//var Utils = require('lib/util/utils.js');
-module.exports = {
-  testTrue: function(client){
-    client.assert.equal(true, true);
-  }
-  /*testFormatElapsedTime : function(client) {
-    var test = client.assert;
-
-    var resultMs = Utils.formatElapsedTime(999);
-    var resultSec = Utils.formatElapsedTime(1999);
-    var resultMin = Utils.formatElapsedTime(122299, true);
-
-    test.equal(resultMs, '999ms');
-    test.equal(resultSec, '1.999s');
-    test.equal(resultMin, '2m 2s / 122299ms');
-  },
-
-  testMakeFnAsync : function(client) {
-    function asynFn(done) {
-      done();
-    }
-
-    function syncFn() {}
-
-    var test = client.assert;
-
-    test.equal(Utils.makeFnAsync(1, asynFn), asynFn);
-
-    var convertedFn = Utils.makeFnAsync(1, syncFn);
-    convertedFn(function() {
-      test.ok('converted fn called');
-    });
-  }*/
-};

LesionTracker/tests/nightwatch/walkthroughs/appLayout.js

@@ -1,14 +0,0 @@
-// add tests to this file using the Nightwatch.js API
-// http://nightwatchjs.org/api
-
-module.exports = {
-  "Layout & Static Pages" : function (client) {
-    client
-      .url("http://localhost:3000")
-      .resizeWindow(1024, 768)
-      .verify.elementPresent("body")
-
-
-      .end();
-  }
-};

OHIFViewer/.gitignore

@@ -1,4 +0,0 @@
-.idea
-.meteor/local
-.meteor/meteorite
-node_modules

OHIFViewer/.meteor/.finished-upgraders

@@ -1,19 +0,0 @@
-# This file contains information which helps Meteor properly upgrade your
-# app when you run 'meteor update'. You should check it into version control
-# with your project.
-
-notices-for-0.9.0
-notices-for-0.9.1
-0.9.4-platform-file
-notices-for-facebook-graph-api-2
-1.2.0-standard-minifiers-package
-1.2.0-meteor-platform-split
-1.2.0-cordova-changes
-1.2.0-breaking-changes
-1.3.0-split-minifiers-package
-1.3.5-remove-old-dev-bundle-link
-1.4.0-remove-old-dev-bundle-link
-1.4.1-add-shell-server-package
-1.4.3-split-account-service-packages
-1.5-add-dynamic-import-package
-1.7-split-underscore-from-meteor-base

OHIFViewer/.meteor/.gitignore

@@ -1,2 +0,0 @@
-dev_bundle
-local

OHIFViewer/.meteor/.id

@@ -1,7 +0,0 @@
-# This file contains a token that is unique to your project.
-# Check it into your repository along with the rest of this directory.
-# It can be used for purposes such as:
-#   - ensuring you don't accidentally deploy one app on top of another
-#   - providing package authors with aggregated statistics
-
-1jfkhvr1ljfqodmpn32m

OHIFViewer/.meteor/packages

@@ -1,55 +0,0 @@
-# Meteor packages used by this project, one per line.
-# Check this file (and the other files in this directory) into your repository.
-#
-# 'meteor add' and 'meteor remove' will edit this file for you,
-# but you can also edit it by hand.
-
-http@1.4.1
-promise@0.11.1
-stylus@2.513.13
-meteor-base@1.4.0
-mobile-experience@1.0.5
-mongo@1.5.0
-blaze-html-templates@1.0.4
-session@1.1.7
-jquery@1.11.10
-tracker@1.2.0
-logging@1.1.20
-reload@1.2.0
-random@1.1.0
-ejson@1.1.0
-spacebars@1.0.12
-check@1.3.1
-ecmascript@0.11.1
-reactive-var@1.0.11
-reactive-dict@1.2.0
-standard-minifier-css@1.4.1
-standard-minifier-js@2.3.4
-
-
-# OHIF Packages
-ohif:polyfill
-ohif:design
-ohif:core
-ohif:commands
-ohif:hotkeys
-ohif:header
-ohif:cornerstone
-ohif:cornerstone-settings
-ohif:viewerbase
-ohif:study-list
-ohif:dicom-services
-ohif:hanging-protocols
-ohif:metadata
-
-twbs:bootstrap
-fortawesome:fontawesome
-momentjs:moment@2.15.1
-aldeed:simple-schema          # Third party package to deal with schemas
-aldeed:template-extension
-gilbertwat:bootstrap3-daterangepicker
-johdirr:meteor-git-rev
-cultofcoders:persistent-session
-shell-server@0.3.1
-underscore
-meteortesting:mocha

OHIFViewer/.meteor/platforms

@@ -1,2 +0,0 @@
-server
-browser

OHIFViewer/.meteor/release

@@ -1 +0,0 @@
-METEOR@1.7.0.3

OHIFViewer/.meteor/versions

@@ -1,137 +0,0 @@
-accounts-base@1.4.2
-aldeed:collection2@2.10.0
-aldeed:collection2-core@1.2.0
-aldeed:schema-deny@1.1.0
-aldeed:schema-index@1.1.1
-aldeed:simple-schema@1.5.4
-aldeed:template-extension@4.1.0
-allow-deny@1.1.0
-amplify@1.0.0
-autoupdate@1.4.1
-babel-compiler@7.1.1
-babel-runtime@1.2.2
-base64@1.0.11
-binary-heap@1.0.10
-blaze@2.3.2
-blaze-html-templates@1.1.2
-blaze-tools@1.0.10
-boilerplate-generator@1.5.0
-caching-compiler@1.1.12
-caching-html-compiler@1.1.3
-callback-hook@1.1.0
-check@1.3.1
-cultofcoders:persistent-session@0.4.5
-dangrossman:bootstrap-daterangepicker@2.1.13
-ddp@1.4.0
-ddp-client@2.3.3
-ddp-common@1.4.0
-ddp-rate-limiter@1.0.7
-ddp-server@2.2.0
-deps@1.0.12
-diff-sequence@1.1.0
-dynamic-import@0.4.1
-ecmascript@0.11.1
-ecmascript-runtime@0.7.0
-ecmascript-runtime-client@0.7.1
-ecmascript-runtime-server@0.7.0
-ejson@1.1.0
-es5-shim@4.8.0
-fastclick@1.0.13
-fortawesome:fontawesome@4.7.0
-geojson-utils@1.0.10
-gilbertwat:bootstrap3-daterangepicker@1.3.21_1
-hot-code-push@1.0.4
-html-tools@1.0.11
-htmljs@1.0.11
-http@1.4.1
-id-map@1.1.0
-iron:controller@1.0.12
-iron:core@1.0.11
-iron:dynamic-template@1.0.12
-iron:layout@1.0.12
-iron:location@1.0.11
-iron:middleware-stack@1.1.0
-iron:router@1.0.13
-iron:url@1.0.11
-johdirr:meteor-git-rev@0.0.4
-jquery@1.11.11
-launch-screen@1.1.1
-livedata@1.0.18
-lmieulet:meteor-coverage@1.1.4
-localstorage@1.2.0
-logging@1.1.20
-mdg:validation-error@0.5.1
-meteor@1.9.0
-meteor-base@1.4.0
-meteor-platform@1.2.6
-meteorhacks:picker@1.0.3
-meteortesting:browser-tests@1.0.0
-meteortesting:mocha@1.0.0
-minifier-css@1.3.1
-minifier-js@2.3.5
-minimongo@1.4.4
-mobile-experience@1.0.5
-mobile-status-bar@1.0.14
-modern-browsers@0.1.1
-modules@0.12.1
-modules-runtime@0.10.2
-momentjs:moment@2.22.2
-mongo@1.5.1
-mongo-dev-server@1.1.0
-mongo-id@1.0.7
-natestrauser:select2@4.0.3
-npm-mongo@3.0.7
-observe-sequence@1.0.16
-ohif:commands@0.0.1
-ohif:core@0.0.1
-ohif:cornerstone@0.0.1
-ohif:cornerstone-settings@0.0.1
-ohif:design@0.0.1
-ohif:dicom-services@0.0.1
-ohif:hanging-protocols@0.0.1
-ohif:header@0.0.1
-ohif:hotkeys@0.0.1
-ohif:log@0.0.1
-ohif:metadata@0.0.1
-ohif:polyfill@0.0.1
-ohif:servers@0.0.1
-ohif:studies@0.0.1
-ohif:study-list@0.0.1
-ohif:themes@0.0.1
-ohif:themes-common@0.0.1
-ohif:viewerbase@0.0.1
-ohif:wadoproxy@0.0.1
-ordered-dict@1.1.0
-practicalmeteor:mocha-core@1.0.1
-promise@0.11.1
-raix:eventemitter@0.1.3
-random@1.1.0
-rate-limit@1.0.9
-reactive-dict@1.2.0
-reactive-var@1.0.11
-reload@1.2.0
-retry@1.1.0
-routepolicy@1.0.13
-service-configuration@1.0.11
-session@1.1.7
-shell-server@0.3.1
-silentcicero:jszip@0.0.4
-socket-stream-client@0.2.2
-spacebars@1.0.15
-spacebars-compiler@1.1.3
-standard-app-packages@1.0.9
-standard-minifier-css@1.4.1
-standard-minifier-js@2.3.4
-stylus@2.513.14
-templating@1.3.2
-templating-compiler@1.3.3
-templating-runtime@1.3.2
-templating-tools@1.1.2
-tracker@1.2.0
-twbs:bootstrap@3.3.6
-ui@1.0.13
-underscore@1.0.10
-url@1.2.0
-validatejs@0.0.1
-webapp@1.6.2
-webapp-hashing@1.0.9

OHIFViewer/bin/medkenOrthanc.bat

@@ -1,2 +0,0 @@
-set METEOR_PACKAGE_DIRS=..\Packages
-meteor --settings ../config/medkenOrthanc.json

OHIFViewer/bin/medkenOrthanc.sh

@@ -1 +0,0 @@
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/medkenOrthanc.json

OHIFViewer/bin/orthanc.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-declare config='../config/orthancDICOMWeb.json'
-
-if [ $# -gt 0 ]; then
-    if [ "$1" = '--dimse' ]; then
-        config="${config%/*}/orthancDIMSE.json"
-        [ -f "$config" ] && echo "DIMSE config file selected: $config"
-    fi
-fi
-
-echo 'Starting Meteor server...'
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings "$config"

OHIFViewer/bin/orthancDICOMWeb.bat

@@ -1,2 +0,0 @@
-set METEOR_PACKAGE_DIRS=..\Packages
-meteor --settings ../config/orthancDICOMWeb.json

OHIFViewer/bin/orthancDICOMWeb.sh

@@ -1,2 +0,0 @@
-echo "Starting Meteor server..."
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/orthancDICOMWeb.json

OHIFViewer/bin/publicOrthancDICOMWeb.sh

@@ -1,2 +0,0 @@
-echo "Starting Meteor server..."
-METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/publicOrthancDICOMWeb.json

OHIFViewer/bin/testPackages.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-##################################################
-# Runs the packages tests
-##################################################
-
-# check execution arguments
-while [ "$1" != "" ]; do
-    PARAM=`echo $1 | awk -F= '{print $1}'`
-    case $PARAM in
-        -c | --coverage)
-            export RUN_COVERAGE=1
-            ;;
-        -v | --verbose)
-            export COVERAGE_VERBOSE=1
-            ;;
-        -s | --spacejam)
-            export RUN_SPACEJAM=1
-            ;;
-        *)
-    esac
-    shift
-done
-
-if [ "$RUN_COVERAGE" == 1 ];
-then
-    # Setting coverage variables
-    app_folder=$(pwd)
-    app_folder+="/packages/ohif-viewerbase/"
-    export COVERAGE_APP_FOLDER=$app_folder
-    export COVERAGE=1
-    echo 'Running meteor-coverage'
-fi
-
-if [ "$RUN_SPACEJAM" == 1 ];
-then
-    spacejam-mocha ./packages/ohif-viewerbase/
-else
-    meteor test-packages --driver-package='cultofcoders:mocha' ./packages/ohif-viewerbase/
-fi

OHIFViewer/client/components/flexboxLayout/flexboxLayout.html

@@ -1,13 +0,0 @@
-<template name="flexboxLayout">
-    <div class="viewerSection">
-        <div class="sidebarMenu sidebar-left {{#if leftSidebarOpen}}sidebar-open{{/if}}">
-            {{> studyBrowser (clone this)}}
-        </div>
-        <div class="mainContent {{#if leftSidebarOpen}}sidebar-left-open{{/if}} {{#if rightSidebarOpen}}sidebar-right-open{{/if}}">
-            {{> viewerMain (clone this)}}
-        </div>
-        <div class="sidebarMenu sidebar-right {{#if rightSidebarOpen}}sidebar-open{{/if}}">
-            {{> protocolEditor (clone this)}}
-        </div>
-    </div>
-</template>

OHIFViewer/client/components/flexboxLayout/flexboxLayout.js

@@ -1,19 +0,0 @@
-Template.flexboxLayout.events({
-    'transitionend .sidebarMenu'(event) {
-        if (!event.target.classList.contains('sidebarMenu')) {
-            return;
-        }
-
-        window.ResizeViewportManager.handleResize();
-    }
-});
-
-Template.flexboxLayout.helpers({
-    leftSidebarOpen() {
-        return Template.instance().data.state.get('leftSidebar');
-    },
-
-    rightSidebarOpen() {
-        return Template.instance().data.state.get('rightSidebar');
-    }
-});

OHIFViewer/client/components/flexboxLayout/flexboxLayout.styl

@@ -1,69 +0,0 @@
-@require '{ohif:design}/app'
-
-$lesionsSidebarMenuWidth = 450px
-
-.viewerSection
-  display: flex
-  flex: 1
-  flex-flow: row nowrap
-  align-items: stretch
-  height: 'calc(100% - %s)' % ($toolbarHeight + $topBarHeight)
-  width: 100%
-
-  .sidebarMenu
-    height: 100%
-    // required transformation to make inner fixed elements relative to this one
-    transform(scale(1))
-    transition($sidebarTransition)
-
-    .sidebar-option
-      height: 100%
-      max-width: inherit
-      position: absolute
-      transform(translateX(100%))
-      transition($sidebarTransition)
-      width: 100%
-
-      &.active
-        transform(translateX(0%))
-
-  .sidebar-left
-    theme('border-right', '%s solid $uiBorderColor' % $uiBorderThickness)
-    flex: 1
-    margin-left: - $studiesSidebarMenuWidth
-    max-width: $studiesSidebarMenuWidth
-    order: 1
-
-    &.sidebar-open
-      margin-left: 0
-
-  .mainContent
-    flex: 1
-    height: 100%
-    order: 2
-    overflow: hidden
-    transition($sidebarTransition)
-    width: 100%
-
-  .sidebar-right
-    flex: 1
-    margin-right: - $lesionsSidebarMenuWidth
-    max-width: $lesionsSidebarMenuWidth
-    order: 3
-    position: relative
-
-    &[data-timepoints="3"]
-      margin-right: - ($lesionsSidebarMenuWidth + 135.5px)
-      max-width: $lesionsSidebarMenuWidth + 135.5px
-
-    &[data-timepoints="4"]
-      margin-right: - ($lesionsSidebarMenuWidth + 270px)
-      max-width: $lesionsSidebarMenuWidth + 270px
-
-    &.sidebar-open
-      margin-right: 0
-
-  .studiesListedChanger
-    theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
-    padding: 20px 10px
-    text-align: center

OHIFViewer/client/components/ohifViewer/ohifViewer.html

@@ -1,25 +0,0 @@
-<template name="ohifViewer">
-    {{#header brandHref='http://ohif.org' headerClasses=instance.headerClasses}}
-        {{#section 'brand'}}
-            <svg class="logo-image">
-                <use xlink:href={{absoluteUrl "packages/ohif_viewerbase/assets/icons.svg#icon-ohif-logo"}}></use>
-            </svg>
-            <div class="logo-text">Open Health Imaging Foundation</div>
-        {{/section}}
-        {{#section 'headerAfterBrand'}}
-            {{#if studyListToggleText}}
-                <a href="#" class="btn studyListLinkSection pull-left js-toggle-studyList">
-                    {{studyListToggleText}}
-                </a>
-            {{/if}}
-        {{/section}}
-        {{#section 'headerMenu'}}
-            <span class="header-options pull-left m-r-1">Options</span>
-            <div class="menu-toggle pull-right">
-                <span class="caret-down"></span>
-            </div>
-        {{/section}}
-    {{/header}}
-
-    {{>Template.dynamic template=(choose this.template 'studylist') data=this}}
-</template>

OHIFViewer/client/components/ohifViewer/ohifViewer.js

@@ -1,78 +0,0 @@
-import { Template } from 'meteor/templating';
-import { Session } from 'meteor/session';
-import { Router } from 'meteor/iron:router';
-import { ReactiveVar } from 'meteor/reactive-var';
-import { OHIF } from 'meteor/ohif:core';
-
-Template.ohifViewer.onCreated(() => {
-    const instance = Template.instance();
-    instance.headerClasses = new ReactiveVar('');
-
-    OHIF.header.dropdown.setItems([{
-        action: () => OHIF.ui.showDialog('serverInformationModal'),
-        text: 'Server Information',
-        icon: 'fa fa-server fa-lg',
-        separatorAfter: true
-    }, {
-        action: () => OHIF.ui.showDialog('themeSelectorModal'),
-        text: 'Themes',
-        iconClasses: 'theme',
-        iconSvgUse: 'packages/ohif_viewerbase/assets/icons.svg#theme',
-        separatorAfter: false
-    }, {
-        action: () => OHIF.ui.showDialog('userPreferencesDialog'),
-        text: 'Preferences',
-        icon: 'fa fa-user',
-        separatorAfter: true
-    }, {
-        action: () => OHIF.ui.showDialog('aboutModal'),
-        text: 'About',
-        icon: 'fa fa-info'
-    }]);
-
-    instance.autorun(() => {
-        const currentRoute = Router.current();
-        if (!currentRoute) return;
-        const routeName = currentRoute.route.getName();
-        const isViewer = routeName.indexOf('viewer') === 0;
-
-        // Add or remove the strech class from body
-        $(document.body)[isViewer ? 'addClass' : 'removeClass']('stretch');
-
-        // Set the header on its bigger version if the viewer is not opened
-        instance.headerClasses.set(isViewer ? '' : 'header-big');
-
-        // Set the viewer open state on session
-        Session.set('ViewerOpened', isViewer);
-    });
-});
-
-Template.ohifViewer.events({
-    'click .js-toggle-studyList'(event, instance) {
-        event.preventDefault();
-        const isViewer = Session.get('ViewerOpened');
-
-        if (isViewer) {
-            Router.go('studylist');
-        } else {
-            const { studyInstanceUids } = OHIF.viewer.data;
-            if (studyInstanceUids) {
-                Router.go('viewerStudies', { studyInstanceUids });
-            }
-        }
-    }
-});
-
-Template.ohifViewer.helpers({
-    studyListToggleText() {
-        const instance = Template.instance();
-        const isViewer = Session.get('ViewerOpened');
-
-        if (isViewer) {
-            instance.hasViewerData = true;
-            return 'Study list';
-        }
-
-        return instance.hasViewerData ? 'Back to viewer' : '';
-    }
-});

OHIFViewer/client/components/ohifViewer/ohifViewer.styl

@@ -1,76 +0,0 @@
-@import "{ohif:design}/app"
-
-body>.header
-
-  .brand
-    height: 30px
-    display: inline-block
-    text-decoration: none
-
-    .logo-image
-      display: inline-block
-      fill: transparent
-      float: left
-      height: 100%
-      margin: 0 8px 0 0
-      width: 30px
-
-    .logo-text
-      display: inline-block
-      font-family: $logoFontFamily
-      font-size: 14px
-      font-weight: $logoFontWeight
-      theme('color', '$textPrimaryColor')
-      line-height: 30px
-
-  a.header-menu
-    theme('color', '$textPrimaryColor')
-
-    .header-options
-      font-size: 13px
-
-    .menu-toggle
-      display: inline-block
-      height: 18px
-
-  .btn
-    theme('color', '$textSecondaryColor')
-    cursor: pointer
-    font-size: 13px
-    font-weight: 500
-    line-height: 26px
-
-    &:hover
-      theme('color', '$hoverColor')
-
-    &:active
-      theme('color', '$activeColor')
-
-  .studyListLinkSection
-    theme('border-left', '%s solid $uiBorderColor' % $uiBorderThickness)
-    margin: 3px 0 0 10px
-    padding: 0 0 0 10px
-
-  &.header-big
-    padding-left: $studyListPadding
-    padding-right: $studyListPadding
-
-    .brand
-      height: 100%
-      width: 80%
-      line-height: $topBarExpandedHeight - 10px
-
-      .logo-image
-        margin: 0 20px 0 0
-        width: 50px
-
-      .logo-text
-        font-size: 30px
-
-    .studyListLinkSection
-      border: none
-      left: 0
-      margin: 0
-      padding: 0
-      position: absolute
-      top: 0

OHIFViewer/client/components/toolbarSection/toolbarSection.html

@@ -1,16 +0,0 @@
-<template name="toolbarSection">
-    <div class="toolbarSection noselect p-x-2">
-        <div class="clearfix">
-            <div class="pull-left m-t-1">
-                {{>roundedButtonGroup leftSidebarToggleButtonData}}
-            </div>
-            {{>toolbarSectionTools toolbarButtons=toolbarButtons}}
-            <div class="pull-right m-t-1 rm-x-1">
-                {{>roundedButtonGroup rightSidebarToggleButtonData}}
-            </div>
-            <div class="pull-right">
-                {{>toolbarSectionTools toolbarButtons=hangingProtocolButtons}}
-            </div>
-        </div>
-    </div>
-</template>

OHIFViewer/client/components/toolbarSection/toolbarSection.js

@@ -1,306 +0,0 @@
-import { Template } from 'meteor/templating';
-import { $ } from 'meteor/jquery';
-
-import { OHIF } from 'meteor/ohif:core';
-import 'meteor/ohif:viewerbase';
-
-function isThereSeries(studies) {
-    if (studies.length === 1) {
-        const study = studies[0];
-
-        if (study.seriesList && study.seriesList.length > 1) {
-            return true;
-        }
-
-        if (study.displaySets && study.displaySets.length > 1) {
-            return true;
-        }
-    }
-
-    return false;
-}
-
-Template.toolbarSection.onCreated(() => {
-    const instance = Template.instance();
-
-    if (OHIF.uiSettings.leftSidebarOpen && isThereSeries(instance.data.studies)) {
-        instance.data.state.set('leftSidebar', 'studies');
-    }
-});
-
-Template.toolbarSection.helpers({
-    leftSidebarToggleButtonData() {
-        const instance = Template.instance();
-        return {
-            toggleable: true,
-            key: 'leftSidebar',
-            value: instance.data.state,
-            options: [{
-                value: 'studies',
-                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-studies',
-                svgWidth: 15,
-                svgHeight: 13,
-                bottomLabel: 'Series'
-            }]
-        };
-    },
-
-    rightSidebarToggleButtonData() {
-        const instance = Template.instance();
-        return {
-            toggleable: true,
-            key: 'rightSidebar',
-            value: instance.data.state,
-            options: [{
-                value: 'hangingprotocols',
-                iconClasses: 'fa fa-cog',
-                bottomLabel: 'Hanging'
-            }]
-        };
-    },
-
-    toolbarButtons() {
-        const extraTools = [];
-
-        extraTools.push({
-            id: 'crosshairs',
-            title: 'Crosshairs',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-crosshairs'
-        });
-
-        extraTools.push({
-            id: 'magnify',
-            title: 'Magnify',
-            classes: 'imageViewerTool toolbarSectionButton',
-            iconClasses: 'fa fa-circle'
-        });
-
-        extraTools.push({
-            id: 'wwwcRegion',
-            title: 'ROI Window',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-square'
-        });
-
-        extraTools.push({
-            id: 'dragProbe',
-            title: 'Probe',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-dot-circle-o'
-        });
-
-        extraTools.push({
-            id: 'ellipticalRoi',
-            title: 'Ellipse',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-circle-o'
-        });
-
-        extraTools.push({
-            id: 'rectangleRoi',
-            title: 'Rectangle',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-square-o'
-        });
-
-        extraTools.push({
-            id: 'toggleDownloadDialog',
-            title: 'Download',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-camera',
-            active: () => $('#downloadDialog').is(':visible')
-        });
-
-        extraTools.push({
-            id: 'invert',
-            title: 'Invert',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-adjust'
-        });
-
-        extraTools.push({
-            id: 'rotateR',
-            title: 'Rotate Right',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-rotate-right'
-        });
-
-        extraTools.push({
-            id: 'flipH',
-            title: 'Flip H',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-flip-horizontal'
-        });
-
-        extraTools.push({
-            id: 'flipV',
-            title: 'Flip V',
-            classes: 'imageViewerCommand',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-flip-vertical'
-        });
-
-        extraTools.push({
-            id: 'clearTools',
-            title: 'Clear',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-trash'
-        });
-
-        const buttonData = [];
-
-        buttonData.push({
-            id: 'stackScroll',
-            title: 'Stack Scroll',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-bars'
-        });
-
-        buttonData.push({
-            id: 'zoom',
-            title: 'Zoom',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-zoom'
-        });
-
-        buttonData.push({
-            id: 'wwwc',
-            title: 'Levels',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-levels'
-        });
-
-        buttonData.push({
-            id: 'pan',
-            title: 'Pan',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-pan'
-        });
-
-        buttonData.push({
-            id: 'length',
-            title: 'Length',
-            classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp'
-        });
-
-        buttonData.push({
-            id: 'annotate',
-            title: 'Annotate',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-non-target'
-        });
-
-        buttonData.push({
-            id: 'angle',
-            title: 'Angle',
-            classes: 'imageViewerTool',
-            iconClasses: 'fa fa-angle-left'
-        });
-
-        buttonData.push({
-            id: 'resetViewport',
-            title: 'Reset',
-            classes: 'imageViewerCommand',
-            iconClasses: 'fa fa-undo'
-        });
-
-        if (!OHIF.uiSettings.displayEchoUltrasoundWorkflow) {
-
-            buttonData.push({
-                id: 'previousDisplaySet',
-                title: 'Previous',
-                classes: 'imageViewerCommand',
-                iconClasses: 'fa fa-toggle-up fa-fw'
-            });
-
-            buttonData.push({
-                id: 'nextDisplaySet',
-                title: 'Next',
-                classes: 'imageViewerCommand',
-                iconClasses: 'fa fa-toggle-down fa-fw'
-            });
-
-            const { isPlaying } = OHIF.viewerbase.viewportUtils;
-            buttonData.push({
-                id: 'toggleCinePlay',
-                title: () => isPlaying() ? 'Stop' : 'Play',
-                classes: 'imageViewerCommand',
-                iconClasses: () => ('fa fa-fw ' + (isPlaying() ? 'fa-stop' : 'fa-play')),
-                active: isPlaying
-            });
-
-            buttonData.push({
-                id: 'toggleCineDialog',
-                title: 'CINE',
-                classes: 'imageViewerCommand',
-                iconClasses: 'fa fa-youtube-play',
-                active: () => $('#cineDialog').is(':visible')
-            });
-        }
-
-        buttonData.push({
-            id: 'layout',
-            title: 'Layout',
-            iconClasses: 'fa fa-th-large',
-            buttonTemplateName: 'layoutButton'
-        });
-
-        buttonData.push({
-            id: 'toggleMore',
-            title: 'More',
-            classes: 'rp-x-1 rm-l-3',
-            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-more',
-            subTools: extraTools
-        });
-
-        return buttonData;
-    },
-
-    hangingProtocolButtons() {
-        let buttonData = [];
-
-        buttonData.push({
-            id: 'previousPresentationGroup',
-            title: 'Prev. Stage',
-            iconClasses: 'fa fa-step-backward',
-            buttonTemplateName: 'previousPresentationGroupButton'
-        });
-
-        buttonData.push({
-            id: 'nextPresentationGroup',
-            title: 'Next Stage',
-            iconClasses: 'fa fa-step-forward',
-            buttonTemplateName: 'nextPresentationGroupButton'
-        });
-
-        return buttonData;
-    }
-
-});
-
-Template.toolbarSection.onRendered(function() {
-    const instance = Template.instance();
-
-    instance.$('#layout').dropdown();
-
-    if (OHIF.uiSettings.displayEchoUltrasoundWorkflow) {
-        OHIF.viewerbase.viewportUtils.toggleCineDialog();
-    }
-
-    // Set disabled/enabled tool buttons that are set in toolManager
-    const states = OHIF.viewerbase.toolManager.getToolDefaultStates();
-    const disabledToolButtons = states.disabledToolButtons;
-    const allToolbarButtons = $('#toolbar').find('button');
-    if (disabledToolButtons && disabledToolButtons.length > 0) {
-        for (let i = 0; i < allToolbarButtons.length; i++) {
-            const toolbarButton = allToolbarButtons[i];
-            $(toolbarButton).prop('disabled', false);
-
-            const index = disabledToolButtons.indexOf($(toolbarButton).attr('id'));
-            if (index !== -1) {
-                $(toolbarButton).prop('disabled', true);
-            }
-        }
-    }
-});

OHIFViewer/client/components/toolbarSection/toolbarSection.styl

@@ -1,13 +0,0 @@
-@require '{ohif:design}/app'
-
-.toolbarSection
-  theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
-  flex: 0 0 auto
-  height: $toolbarHeight
-  padding-top: 6px
-  position: relative
-  transition(height 300ms ease)
-  width: 100%
-
-  &.expanded
-    height: $toolbarHeight + $toolbarDrawerHeight