diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml new file mode 100644 index 000000000..1558f74c4 --- /dev/null +++ b/.github/workflows/image_build_push.yaml @@ -0,0 +1,15 @@ +name: Build Image and Push to Quay + +on: push + +jobs: + ci: + name: Build Image and Push to Quay + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + OVERRIDE_REPO_NAME: "ohdsi-atlas" + secrets: + ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} + ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} + QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} + QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 000000000..8412d22a4 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,11 @@ +repos: +- repo: git@github.com:Yelp/detect-secrets + rev: v1.3.0 + hooks: + - id: detect-secrets + args: ['--baseline', '.secrets.baseline'] +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.3.0 + hooks: + - id: no-commit-to-branch + args: [--branch, develop, --branch, master, --pattern, release/.*] diff --git a/.secrets.baseline b/.secrets.baseline new file mode 100644 index 000000000..1e78da464 --- /dev/null +++ b/.secrets.baseline @@ -0,0 +1,1535 @@ +{ + "version": "1.3.0", + "plugins_used": [ + { + "name": "ArtifactoryDetector" + }, + { + "name": "AWSKeyDetector" + }, + { + "name": "AzureStorageKeyDetector" + }, + { + "name": "Base64HighEntropyString", + "limit": 4.5 + }, + { + "name": "BasicAuthDetector" + }, + { + "name": "CloudantDetector" + }, + { + "name": "GitHubTokenDetector" + }, + { + "name": "HexHighEntropyString", + "limit": 3.0 + }, + { + "name": "IbmCloudIamDetector" + }, + { + "name": "IbmCosHmacDetector" + }, + { + "name": "JwtTokenDetector" + }, + { + "name": "KeywordDetector", + "keyword_exclude": "" + }, + { + "name": "MailchimpDetector" + }, + { + "name": "NpmDetector" + }, + { + "name": "PrivateKeyDetector" + }, + { + "name": "SendGridDetector" + }, + { + "name": "SlackDetector" + }, + { + "name": "SoftlayerDetector" + }, + { + "name": "SquareOAuthDetector" + }, + { + "name": "StripeDetector" + }, + { + "name": "TwilioKeyDetector" + } + ], + "filters_used": [ + { + "path": "detect_secrets.filters.allowlist.is_line_allowlisted" + }, + { + "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", + "min_level": 2 + }, + { + "path": "detect_secrets.filters.heuristic.is_indirect_reference" + }, + { + "path": "detect_secrets.filters.heuristic.is_likely_id_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_lock_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_potential_uuid" + }, + { + "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign" + }, + { + "path": "detect_secrets.filters.heuristic.is_sequential_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_swagger_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_templated_secret" + } + ], + "results": { + "js/assets/d3-scale-chromatic.1.3.0.min.js": [ + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "010ee250868c6ff616ec04de5c6167a7679af561", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "02a3dd3d953d09d75ad25b2320b04c582257f4a7", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "02efb92f0acc8db523c7e9b8a38f66304a038dcd", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": 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+ { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "e1f8501cbc2b1daef351976b6ce8f28d930f8b3b", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "e2fa12f055b9832acb7054f9af167237ca986cbd", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "e5022023bbfcc703661e78432e4ddc0b27eeef62", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "e7153ba2a94435a5ba0b1f84a69890e31199f056", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "e79d2194550ee64c3275e88a61fda3374847adf1", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "ec204715a8ed5e717806d6ed42756a969e823fe5", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "ed1484010237fdeef3bb0120bf0959c36db271cc", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "ee4c8c0a98c0bb4902050a178ac2d7bcac7d1d7f", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "f08200ea97cd5fdcc77113dbead01339b9a885f6", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": 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+ { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "f8c386d4b56c87b8ef68e4527e1f6c769f7dba02", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "fa921fd526e96ff82f663d844ec087733da325c5", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "fad491a101771adad3f61b91a42c5a5a7734887e", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "fcbc10d3a08fe17a25321109cf31bb4d77956f06", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "fd5e33d17b8fd268351e3d1eb47c20187997e8e9", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "fe686551be16c9c3eba03634795b41637038794b", + "is_verified": false, + "line_number": 2 + }, + { + "type": "Hex High Entropy String", + "filename": "js/assets/d3-scale-chromatic.1.3.0.min.js", + "hashed_secret": "ff811fe23f85e13980baeae3e37f0c2146454e55", + "is_verified": false, + "line_number": 2 + } + ], + "js/pages/characterizations/stubs/characterization-results-data.r": [ + { + "type": "Secret Keyword", + "filename": "js/pages/characterizations/stubs/characterization-results-data.r", + "hashed_secret": "bb470fb830643e2e1a36d81473cf03ae18733dfd", + "is_verified": false, + "line_number": 7 + } + ] + }, + "generated_at": "2022-07-30T01:48:55Z" +} diff --git a/Dockerfile b/Dockerfile index 04f5d9692..6e36da3ec 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Build the source -FROM docker.io/library/node:18.14.1-alpine@sha256:045b1a1c90bdfd8fcaad0769922aa16c401e31867d8bf5833365b0874884bbae as builder +FROM quay.io/cdis/node:14-alpine as builder WORKDIR /code @@ -26,7 +26,7 @@ RUN find . -type f "(" \ | xargs -0 -n 1 gzip -kf # Production Nginx image -FROM docker.io/nginxinc/nginx-unprivileged:1.27.2-alpine +FROM quay.io/cdis/nginx-unprivileged:1.20-alpine LABEL org.opencontainers.image.title="OHDSI-Atlas" LABEL org.opencontainers.image.authors="Joris Borgdorff , Lee Evans - www.ltscomputingllc.com, Shaun Turner" diff --git a/NOTICE b/NOTICE new file mode 100644 index 000000000..d7b00465b --- /dev/null +++ b/NOTICE @@ -0,0 +1,7 @@ +Copyright 2015-2025 University of Chicago + +Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. diff --git a/docker/nginx-default.conf b/docker/nginx-default.conf index 8131c07bc..427b7928f 100644 --- a/docker/nginx-default.conf +++ b/docker/nginx-default.conf @@ -5,6 +5,7 @@ server { location ~ ^.*[^/]$ { try_files $uri @rewrite; + add_header Cache-Control "no-cache, must-revalidate"; } location @rewrite { diff --git a/index.html b/index.html index 1938905f2..38ff7de20 100644 --- a/index.html +++ b/index.html @@ -41,12 +41,16 @@
+ + + +
@@ -55,7 +59,7 @@
open source software
provided by
-
+
OHDSI logo with link to OHDSI site
join the journey
diff --git a/js/Application.js b/js/Application.js index eb95f499d..8544059e9 100644 --- a/js/Application.js +++ b/js/Application.js @@ -96,6 +96,11 @@ define( }); this.companyInfoTemplate = config.companyInfoCustomHtmlTemplate; this.showCompanyInfo = config.showCompanyInfo; + this.isLoggedIn = ko.computed(() => authApi.isAuthenticated()); + } + + timeToExpire() { + return authApi.tokenExpirationDate() - new Date(); } /** @@ -136,6 +141,24 @@ define( this.attachGlobalEventListeners(); await executionService.checkExecutionEngineStatus(authApi.isAuthenticated()); + // Add user interaction listener that keeps refreshing the token as long + // as the user is active (either moving mouse, navigating with keyboard and/or typing): + var userInteractionCount = 0; + console.log("Adding user interaction listeners..."); + ["mouseover", "keydown", "focusin"].forEach(eventType => { + window.addEventListener(eventType, (event) => { + userInteractionCount++; + if (userInteractionCount % 30 == 0) { + console.log(">>> Checking user token...."); + userInteractionCount = 0; + // Refresh the Atlas token if it is close to expiring: + if (authApi.isAuthenticated() && this.timeToExpire() < config.refreshTokenThreshold) { + console.log(">>> Token close to expiring. Refreshing user token...."); + authApi.refreshToken(); + } + } + }); + }); resolve(); }); diff --git a/js/components/analysisExecution/analysis-execution-list.html b/js/components/analysisExecution/analysis-execution-list.html index 8fcddaac4..542a71df1 100644 --- a/js/components/analysisExecution/analysis-execution-list.html +++ b/js/components/analysisExecution/analysis-execution-list.html @@ -9,9 +9,12 @@

{ if (id) { this.loadData(); @@ -143,7 +145,7 @@ define([ this.execColumns = tableColumns.map(col => execColumnsMap[col]); this.isViewGenerationsPermitted = ko.computed( - () => (this.analysisId() ? this.PermissionService.isPermittedListGenerations(this.analysisId()) : true) + () => (this.characterizationId() ? this.PermissionService.isPermittedListGenerations(this.characterizationId()) : true) ); this.isViewGenerationsPermitted && this.startPolling(); @@ -165,11 +167,9 @@ define([ async loadData({ silently = false } = {}) { !silently && this.loading(true); - const analysisId = this.analysisId(); - try { const allSources = await SourceService.loadSourceList(); - const executionList = await this.ExecutionService.listExecutions(analysisId); + const executionList = await this.ExecutionService.listExecutions(this.characterizationId()); let sourceList = allSources.filter(({ daimons = [] }) => { const daimonTypes = daimons.map(({ daimonType }) => daimonType); return ['CDM', 'Results'].every(daimonType => daimonTypes.includes(daimonType)); @@ -204,7 +204,7 @@ define([ try { this.executionDesign(null); this.isExecutionDesignShown(true); - const data = await this.ExecutionService.loadExportDesignByGeneration(executionId); + const data = await this.ExecutionService.loadExportDesignByGeneration(this.characterizationId(), executionId); this.executionDesign(data); } catch (err) { console.error(err); @@ -230,15 +230,15 @@ define([ toggleSection(sourceId) { if (parseInt(this.selectedSourceId()) === sourceId) { this.selectedSourceId(null); - CommonUtils.routeTo(`${this.resultsPathPrefix}${this.analysisId()}/executions`); + CommonUtils.routeTo(`${this.resultsPathPrefix}${this.characterizationId()}/executions`); } else { this.selectedSourceId(sourceId); - CommonUtils.routeTo(`${this.resultsPathPrefix}${this.analysisId()}/executions/${sourceId}`); + CommonUtils.routeTo(`${this.resultsPathPrefix}${this.characterizationId()}/executions/${sourceId}`); } } isGenerationPermitted(sourceKey) { - const isPermitted = this.PermissionService.isPermittedGenerate(this.analysisId(), sourceKey); + const isPermitted = this.PermissionService.isPermittedGenerate(this.characterizationId(), sourceKey); if (this.extraExecutionPermissions) { return isPermitted && this.extraExecutionPermissions(); } @@ -246,7 +246,7 @@ define([ } isResultsViewPermitted(sourceKey) { - return this.PermissionService.isPermittedResults(sourceKey); + return this.PermissionService.isPermittedResults(this.characterizationId(), sourceKey); } getDisableReason(sourceKey) { @@ -265,7 +265,7 @@ define([ await ExecutionUtils.StartExecution(executionGroup); } executionGroup.status(this.executionStatuses.PENDING); - const data = await this.ExecutionService.generate(this.analysisId(), sourceKey); + const data = await this.ExecutionService.generate(this.characterizationId(), sourceKey); if (data) { JobDetailsService.createJob(data); this.loadData({silently: true}); @@ -279,7 +279,7 @@ define([ cancelGenerate(sourceKey) { this.stopping({...this.stopping(), [sourceKey]: true}); if (confirm(ko.i18n('components.analysisExecution.stopGenerationConfirmation', 'Do you want to stop generation?')())) { - this.ExecutionService.cancelGeneration(this.analysisId(), sourceKey); + this.ExecutionService.cancelGeneration(this.characterizationId(), sourceKey); } else { this.stopping({...this.stopping(), [sourceKey]: false}); } @@ -319,7 +319,7 @@ define([ } goToResults(executionId) { - CommonUtils.routeTo(`${this.resultsPathPrefix}${this.analysisId()}/results/${executionId}`); + CommonUtils.routeTo(`${this.resultsPathPrefix}${this.characterizationId()}/results/${executionId}`); } findLatestSubmission(sourceKey) { diff --git a/js/components/authorship.html b/js/components/authorship.html index d881bdcb4..e4366ca6e 100644 --- a/js/components/authorship.html +++ b/js/components/authorship.html @@ -2,7 +2,7 @@
, diff --git a/js/components/cohortbuilder/components/CohortExpressionEditorTemplate.html b/js/components/cohortbuilder/components/CohortExpressionEditorTemplate.html index ead0c21bd..4f9741635 100644 --- a/js/components/cohortbuilder/components/CohortExpressionEditorTemplate.html +++ b/js/components/cohortbuilder/components/CohortExpressionEditorTemplate.html @@ -50,11 +50,11 @@
- - @@ -62,7 +62,7 @@
- @@ -200,7 +200,7 @@
  • - +
    • diff --git a/js/components/cohortbuilder/components/ConceptSetQuickviewTemplate.html b/js/components/cohortbuilder/components/ConceptSetQuickviewTemplate.html index 9a0fcfd65..4e5c62d88 100644 --- a/js/components/cohortbuilder/components/ConceptSetQuickviewTemplate.html +++ b/js/components/cohortbuilder/components/ConceptSetQuickviewTemplate.html @@ -9,9 +9,9 @@
    - - - + + + diff --git a/js/components/cohortbuilder/components/ConceptSetSelector.js b/js/components/cohortbuilder/components/ConceptSetSelector.js index 9f5c13421..80b88c564 100644 --- a/js/components/cohortbuilder/components/ConceptSetSelector.js +++ b/js/components/cohortbuilder/components/ConceptSetSelector.js @@ -51,7 +51,23 @@ define([ ); }); - self.itemClicked = function (item) { + self.itemClicked = function (item, event) { + // Check for key presses + if (event.type === "keydown") { + const key = event.key; + if (key === "Enter" || key === " ") { + event.preventDefault(); // Prevent default behavior + event.target.click(); // Simulate a click, which closes the menu + return true; + } else if (key === "ArrowRight") { + event.preventDefault(); + const hoverEvent = new Event('mouseover', { bubbles: true }); + event.target.dispatchEvent(hoverEvent); // Simulate hover. + return true; + } else { + return true; // Let other keys propagate normally + } + } self.conceptSetId(item.id); self.previewVisible(false); }; diff --git a/js/components/cohortbuilder/components/ConceptSetSelectorTemplate.html b/js/components/cohortbuilder/components/ConceptSetSelectorTemplate.html index 74a77d520..fe209de16 100644 --- a/js/components/cohortbuilder/components/ConceptSetSelectorTemplate.html +++ b/js/components/cohortbuilder/components/ConceptSetSelectorTemplate.html @@ -13,34 +13,36 @@
      -