├── .git-blame-ignore-revs ├── .github ├── dependabot.yml └── workflows │ ├── ci-build.yml │ ├── codeql-analysis.yml │ └── docker.yml ├── .gitignore ├── .mergify.yml ├── .mvn └── wrapper │ └── maven-wrapper.properties ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── ISSUE_TEMPLATE.md ├── LICENSE.md ├── NOTICE.md ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── docker-compose.yml ├── docs ├── diagrams │ ├── README.md │ ├── cwlviewer.svg │ ├── cwlviewer_flowchat_01.png │ ├── cwlviewer_flowchat_02.png │ └── cwlviewer_flowchat_03.png └── mongo-to-postgres │ ├── .gitignore │ ├── README.md │ ├── mongo_to_pg.ipynb │ ├── mongo_to_pg.py │ └── requirements.txt ├── dump.py ├── load.py ├── mvnw ├── mvnw.cmd ├── pg_hba.conf ├── pom.xml ├── src ├── main │ ├── java │ │ └── org │ │ │ └── commonwl │ │ │ └── view │ │ │ ├── CwlViewerApplication.java │ │ │ ├── GlobalControllerErrorHandling.java │ │ │ ├── PageController.java │ │ │ ├── Scheduler.java │ │ │ ├── WebConfig.java │ │ │ ├── cwl │ │ │ ├── CWLElement.java │ │ │ ├── CWLNotAWorkflowException.java │ │ │ ├── CWLProcess.java │ │ │ ├── CWLService.java │ │ │ ├── CWLStep.java │ │ │ ├── CWLTool.java │ │ │ ├── CWLToolRunner.java │ │ │ ├── CWLToolStatus.java │ │ │ ├── CWLValidationException.java │ │ │ └── RDFService.java │ │ │ ├── docker │ │ │ └── DockerService.java │ │ │ ├── git │ │ │ ├── GitConfig.java │ │ │ ├── GitDetails.java │ │ │ ├── GitLicenseException.java │ │ │ ├── GitSemaphore.java │ │ │ ├── GitService.java │ │ │ └── GitType.java │ │ │ ├── graphviz │ │ │ ├── DotWriter.java │ │ │ ├── GraphVizService.java │ │ │ ├── ModelDotWriter.java │ │ │ └── RDFDotWriter.java │ │ │ ├── researchobject │ │ │ ├── HashableAgent.java │ │ │ ├── ROBundleFactory.java │ │ │ ├── ROBundleNotFoundException.java │ │ │ └── ROBundleService.java │ │ │ ├── util │ │ │ ├── BaseEntity.java │ │ │ ├── FileUtils.java │ │ │ ├── LicenseUtils.java │ │ │ └── StreamGobbler.java │ │ │ └── workflow │ │ │ ├── MultipleWorkflowsException.java │ │ │ ├── QueuedWorkflow.java │ │ │ ├── QueuedWorkflowRepository.java │ │ │ ├── QueuedWorkflowRepositoryCustom.java │ │ │ ├── QueuedWorkflowRepositoryImpl.java │ │ │ ├── RepresentationNotFoundException.java │ │ │ ├── Workflow.java │ │ │ ├── WorkflowController.java │ │ │ ├── WorkflowForm.java │ │ │ ├── WorkflowFormValidator.java │ │ │ ├── WorkflowJSONController.java │ │ │ ├── WorkflowNotFoundException.java │ │ │ ├── WorkflowOverview.java │ │ │ ├── WorkflowPermalinkController.java │ │ │ ├── WorkflowRepository.java │ │ │ ├── WorkflowRepositoryCustom.java │ │ │ ├── WorkflowRepositoryImpl.java │ │ │ └── WorkflowService.java │ └── resources │ │ ├── application.properties │ │ ├── db │ │ └── changelog │ │ │ ├── db.changelog.xml │ │ │ └── migrations │ │ │ └── 00001_schema_ddl.sql │ │ ├── favicon.ico │ │ ├── logback.xml │ │ ├── messages.properties │ │ ├── static │ │ ├── bower_components │ │ │ ├── bootstrap │ │ │ │ ├── .bower.json │ │ │ │ ├── CHANGELOG.md │ │ │ │ ├── Gemfile │ │ │ │ ├── Gemfile.lock │ │ │ │ ├── Gruntfile.js │ │ │ │ ├── ISSUE_TEMPLATE.md │ │ │ │ ├── LICENSE │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ ├── dist │ │ │ │ │ ├── css │ │ │ │ │ │ ├── bootstrap-theme.css │ │ │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ │ │ ├── bootstrap-theme.min.css.map │ │ │ │ │ │ ├── bootstrap.css │ │ │ │ │ │ ├── bootstrap.css.map │ │ │ │ │ │ ├── bootstrap.min.css │ │ │ │ │ │ └── bootstrap.min.css.map │ │ │ │ │ ├── fonts │ │ │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ │ │ └── js │ │ │ │ │ │ ├── bootstrap.js │ │ │ │ │ │ ├── bootstrap.min.js │ │ │ │ │ │ └── npm.js │ │ │ │ ├── fonts │ │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ │ ├── grunt │ │ │ │ │ ├── .jshintrc │ │ │ │ │ ├── bs-commonjs-generator.js │ │ │ │ │ ├── bs-glyphicons-data-generator.js │ │ │ │ │ ├── bs-lessdoc-parser.js │ │ │ │ │ ├── bs-raw-files-generator.js │ │ │ │ │ ├── change-version.js │ │ │ │ │ ├── configBridge.json │ │ │ │ │ ├── npm-shrinkwrap.json │ │ │ │ │ └── sauce_browsers.yml │ │ │ │ ├── js │ │ │ │ │ ├── .jscsrc │ │ │ │ │ ├── .jshintrc │ │ │ │ │ ├── affix.js │ │ │ │ │ ├── alert.js │ │ │ │ │ ├── button.js │ │ │ │ │ ├── carousel.js │ │ │ │ │ ├── collapse.js │ │ │ │ │ ├── dropdown.js │ │ │ │ │ ├── modal.js │ │ │ │ │ ├── popover.js │ │ │ │ │ ├── scrollspy.js │ │ │ │ │ ├── tab.js │ │ │ │ │ ├── tooltip.js │ │ │ │ │ └── transition.js │ │ │ │ ├── less │ │ │ │ │ ├── .csscomb.json │ │ │ │ │ ├── .csslintrc │ │ │ │ │ ├── alerts.less │ │ │ │ │ ├── badges.less │ │ │ │ │ ├── bootstrap.less │ │ │ │ │ ├── breadcrumbs.less │ │ │ │ │ ├── button-groups.less │ │ │ │ │ ├── buttons.less │ │ │ │ │ ├── carousel.less │ │ │ │ │ ├── close.less │ │ │ │ │ ├── code.less │ │ │ │ │ ├── component-animations.less │ │ │ │ │ ├── dropdowns.less │ │ │ │ │ ├── forms.less │ │ │ │ │ ├── glyphicons.less │ │ │ │ │ ├── grid.less │ │ │ │ │ ├── input-groups.less │ │ │ │ │ ├── jumbotron.less │ │ │ │ │ ├── labels.less │ │ │ │ │ ├── list-group.less │ │ │ │ │ ├── media.less │ │ │ │ │ ├── mixins.less │ │ │ │ │ ├── mixins │ │ │ │ │ │ ├── alerts.less │ │ │ │ │ │ ├── background-variant.less │ │ │ │ │ │ ├── border-radius.less │ │ │ │ │ │ ├── buttons.less │ │ │ │ │ │ ├── center-block.less │ │ │ │ │ │ ├── clearfix.less │ │ │ │ │ │ ├── forms.less │ │ │ │ │ │ ├── gradients.less │ │ │ │ │ │ ├── grid-framework.less │ │ │ │ │ │ ├── grid.less │ │ │ │ │ │ ├── hide-text.less │ │ │ │ │ │ ├── image.less │ │ │ │ │ │ ├── labels.less │ │ │ │ │ │ ├── list-group.less │ │ │ │ │ │ ├── nav-divider.less │ │ │ │ │ │ ├── nav-vertical-align.less │ │ │ │ │ │ ├── opacity.less │ │ │ │ │ │ ├── pagination.less │ │ │ │ │ │ ├── panels.less │ │ │ │ │ │ ├── progress-bar.less │ │ │ │ │ │ ├── reset-filter.less │ │ │ │ │ │ ├── reset-text.less │ │ │ │ │ │ ├── resize.less │ │ │ │ │ │ ├── responsive-visibility.less │ │ │ │ │ │ ├── size.less │ │ │ │ │ │ ├── tab-focus.less │ │ │ │ │ │ ├── table-row.less │ │ │ │ │ │ ├── text-emphasis.less │ │ │ │ │ │ ├── text-overflow.less │ │ │ │ │ │ └── vendor-prefixes.less │ │ │ │ │ ├── modals.less │ │ │ │ │ ├── navbar.less │ │ │ │ │ ├── navs.less │ │ │ │ │ ├── normalize.less │ │ │ │ │ ├── pager.less │ │ │ │ │ ├── pagination.less │ │ │ │ │ ├── panels.less │ │ │ │ │ ├── popovers.less │ │ │ │ │ ├── print.less │ │ │ │ │ ├── progress-bars.less │ │ │ │ │ ├── responsive-embed.less │ │ │ │ │ ├── responsive-utilities.less │ │ │ │ │ ├── scaffolding.less │ │ │ │ │ ├── tables.less │ │ │ │ │ ├── theme.less │ │ │ │ │ ├── thumbnails.less │ │ │ │ │ ├── tooltip.less │ │ │ │ │ ├── type.less │ │ │ │ │ ├── utilities.less │ │ │ │ │ ├── variables.less │ │ │ │ │ └── wells.less │ │ │ │ ├── nuget │ │ │ │ │ ├── MyGet.ps1 │ │ │ │ │ ├── bootstrap.less.nuspec │ │ │ │ │ └── bootstrap.nuspec │ │ │ │ ├── package.js │ │ │ │ └── package.json │ │ │ ├── hammerjs │ │ │ │ ├── .bower.json │ │ │ │ ├── CHANGELOG.md │ │ │ │ ├── CONTRIBUTING.md │ │ │ │ ├── LICENSE.md │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ ├── changelog.js │ │ │ │ ├── hammer.js │ │ │ │ ├── hammer.min.js │ │ │ │ ├── hammer.min.js.map │ │ │ │ └── hammer.min.map │ │ │ ├── highlightjs │ │ │ │ ├── .bower.json │ │ │ │ ├── LICENSE │ │ │ │ ├── Makefile │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ ├── component.json │ │ │ │ ├── composer.json │ │ │ │ ├── highlight.pack.js │ │ │ │ ├── highlight.pack.min.js │ │ │ │ ├── package.json │ │ │ │ └── styles │ │ │ │ │ ├── agate.css │ │ │ │ │ ├── androidstudio.css │ │ │ │ │ ├── arduino-light.css │ │ │ │ │ ├── arta.css │ │ │ │ │ ├── ascetic.css │ │ │ │ │ ├── atelier-cave-dark.css │ │ │ │ │ ├── atelier-cave-light.css │ │ │ │ │ ├── atelier-cave.dark.css │ │ │ │ │ ├── atelier-cave.light.css │ │ │ │ │ ├── atelier-dune-dark.css │ │ │ │ │ ├── atelier-dune-light.css │ │ │ │ │ ├── atelier-dune.dark.css │ │ │ │ │ ├── atelier-dune.light.css │ │ │ │ │ ├── atelier-estuary-dark.css │ │ │ │ │ ├── atelier-estuary-light.css │ │ │ │ │ ├── atelier-estuary.dark.css │ │ │ │ │ ├── atelier-estuary.light.css │ │ │ │ │ ├── atelier-forest-dark.css │ │ │ │ │ ├── atelier-forest-light.css │ │ │ │ │ ├── atelier-forest.dark.css │ │ │ │ │ ├── atelier-forest.light.css │ │ │ │ │ ├── atelier-heath-dark.css │ │ │ │ │ ├── atelier-heath-light.css │ │ │ │ │ ├── atelier-heath.dark.css │ │ │ │ │ ├── atelier-heath.light.css │ │ │ │ │ ├── atelier-lakeside-dark.css │ │ │ │ │ ├── atelier-lakeside-light.css │ │ │ │ │ ├── atelier-lakeside.dark.css │ │ │ │ │ ├── atelier-lakeside.light.css │ │ │ │ │ ├── atelier-plateau-dark.css │ │ │ │ │ ├── atelier-plateau-light.css │ │ │ │ │ ├── atelier-plateau.dark.css │ │ │ │ │ ├── atelier-plateau.light.css │ │ │ │ │ ├── atelier-savanna-dark.css │ │ │ │ │ ├── atelier-savanna-light.css │ │ │ │ │ ├── atelier-savanna.dark.css │ │ │ │ │ ├── atelier-savanna.light.css │ │ │ │ │ ├── atelier-seaside-dark.css │ │ │ │ │ ├── atelier-seaside-light.css │ │ │ │ │ ├── atelier-seaside.dark.css │ │ │ │ │ ├── atelier-seaside.light.css │ │ │ │ │ ├── atelier-sulphurpool-dark.css │ │ │ │ │ ├── atelier-sulphurpool-light.css │ │ │ │ │ ├── atelier-sulphurpool.dark.css │ │ │ │ │ ├── atelier-sulphurpool.light.css │ │ │ │ │ ├── atom-one-dark.css │ │ │ │ │ ├── atom-one-light.css │ │ │ │ │ ├── brown-paper.css │ │ │ │ │ ├── brown-papersq.png │ │ │ │ │ ├── brown_paper.css │ │ │ │ │ ├── brown_papersq.png │ │ │ │ │ ├── codepen-embed.css │ │ │ │ │ ├── color-brewer.css │ │ │ │ │ ├── darcula.css │ │ │ │ │ ├── dark.css │ │ │ │ │ ├── darkula.css │ │ │ │ │ ├── default.css │ │ │ │ │ ├── docco.css │ │ │ │ │ ├── dracula.css │ │ │ │ │ ├── far.css │ │ │ │ │ ├── foundation.css │ │ │ │ │ ├── github-gist.css │ │ │ │ │ ├── github.css │ │ │ │ │ ├── googlecode.css │ │ │ │ │ ├── grayscale.css │ │ │ │ │ ├── gruvbox-dark.css │ │ │ │ │ ├── gruvbox-light.css │ │ │ │ │ ├── hopscotch.css │ │ │ │ │ ├── hybrid.css │ │ │ │ │ ├── idea.css │ │ │ │ │ ├── ir-black.css │ │ │ │ │ ├── ir_black.css │ │ │ │ │ ├── kimbie.dark.css │ │ │ │ │ ├── kimbie.light.css │ │ │ │ │ ├── magula.css │ │ │ │ │ ├── mono-blue.css │ │ │ │ │ ├── monokai-sublime.css │ │ │ │ │ ├── monokai.css │ │ │ │ │ ├── monokai_sublime.css │ │ │ │ │ ├── obsidian.css │ │ │ │ │ ├── ocean.css │ │ │ │ │ ├── paraiso-dark.css │ │ │ │ │ ├── paraiso-light.css │ │ │ │ │ ├── paraiso.dark.css │ │ │ │ │ ├── paraiso.light.css │ │ │ │ │ ├── pojoaque.css │ │ │ │ │ ├── pojoaque.jpg │ │ │ │ │ ├── purebasic.css │ │ │ │ │ ├── qtcreator_dark.css │ │ │ │ │ ├── qtcreator_light.css │ │ │ │ │ ├── railscasts.css │ │ │ │ │ ├── rainbow.css │ │ │ │ │ ├── routeros.css │ │ │ │ │ ├── school-book.css │ │ │ │ │ ├── school-book.png │ │ │ │ │ ├── school_book.css │ │ │ │ │ ├── school_book.png │ │ │ │ │ ├── solarized-dark.css │ │ │ │ │ ├── solarized-light.css │ │ │ │ │ ├── solarized_dark.css │ │ │ │ │ ├── solarized_light.css │ │ │ │ │ ├── sunburst.css │ │ │ │ │ ├── tomorrow-night-blue.css │ │ │ │ │ ├── tomorrow-night-bright.css │ │ │ │ │ ├── tomorrow-night-eighties.css │ │ │ │ │ ├── tomorrow-night.css │ │ │ │ │ ├── tomorrow.css │ │ │ │ │ ├── vs.css │ │ │ │ │ ├── vs2015.css │ │ │ │ │ ├── xcode.css │ │ │ │ │ ├── xt256.css │ │ │ │ │ └── zenburn.css │ │ │ ├── jquery-svg │ │ │ │ ├── .bower.json │ │ │ │ ├── README.md │ │ │ │ ├── jquery.svg.css │ │ │ │ ├── jquery.svg.js │ │ │ │ ├── jquery.svg.min.js │ │ │ │ ├── jquery.svganim.js │ │ │ │ ├── jquery.svganim.min.js │ │ │ │ ├── jquery.svgdom.js │ │ │ │ ├── jquery.svgdom.min.js │ │ │ │ ├── jquery.svgfilter.js │ │ │ │ ├── jquery.svgfilter.min.js │ │ │ │ ├── jquery.svggraph.js │ │ │ │ ├── jquery.svggraph.min.js │ │ │ │ ├── jquery.svgplot.js │ │ │ │ ├── jquery.svgplot.min.js │ │ │ │ ├── kbw.svg.jquery.json │ │ │ │ ├── lion.svg │ │ │ │ └── svgBasic.html │ │ │ ├── jquery │ │ │ │ ├── .bower.json │ │ │ │ ├── AUTHORS.txt │ │ │ │ ├── LICENSE.txt │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ ├── dist │ │ │ │ │ ├── core.js │ │ │ │ │ ├── jquery.js │ │ │ │ │ ├── jquery.min.js │ │ │ │ │ ├── jquery.min.map │ │ │ │ │ ├── jquery.slim.js │ │ │ │ │ ├── jquery.slim.min.js │ │ │ │ │ └── jquery.slim.min.map │ │ │ │ ├── external │ │ │ │ │ └── sizzle │ │ │ │ │ │ ├── LICENSE.txt │ │ │ │ │ │ └── dist │ │ │ │ │ │ ├── sizzle.js │ │ │ │ │ │ ├── sizzle.min.js │ │ │ │ │ │ └── sizzle.min.map │ │ │ │ └── src │ │ │ │ │ ├── .eslintrc.json │ │ │ │ │ ├── ajax.js │ │ │ │ │ ├── ajax │ │ │ │ │ ├── jsonp.js │ │ │ │ │ ├── load.js │ │ │ │ │ ├── parseXML.js │ │ │ │ │ ├── script.js │ │ │ │ │ ├── var │ │ │ │ │ │ ├── location.js │ │ │ │ │ │ ├── nonce.js │ │ │ │ │ │ └── rquery.js │ │ │ │ │ └── xhr.js │ │ │ │ │ ├── attributes.js │ │ │ │ │ ├── attributes │ │ │ │ │ ├── attr.js │ │ │ │ │ ├── classes.js │ │ │ │ │ ├── prop.js │ │ │ │ │ ├── support.js │ │ │ │ │ └── val.js │ │ │ │ │ ├── callbacks.js │ │ │ │ │ ├── core.js │ │ │ │ │ ├── core │ │ │ │ │ ├── DOMEval.js │ │ │ │ │ ├── access.js │ │ │ │ │ ├── init.js │ │ │ │ │ ├── parseHTML.js │ │ │ │ │ ├── ready-no-deferred.js │ │ │ │ │ ├── ready.js │ │ │ │ │ ├── readyException.js │ │ │ │ │ ├── stripAndCollapse.js │ │ │ │ │ ├── support.js │ │ │ │ │ └── var │ │ │ │ │ │ └── rsingleTag.js │ │ │ │ │ ├── css.js │ │ │ │ │ ├── css │ │ │ │ │ ├── addGetHookIf.js │ │ │ │ │ ├── adjustCSS.js │ │ │ │ │ ├── curCSS.js │ │ │ │ │ ├── hiddenVisibleSelectors.js │ │ │ │ │ ├── showHide.js │ │ │ │ │ ├── support.js │ │ │ │ │ └── var │ │ │ │ │ │ ├── cssExpand.js │ │ │ │ │ │ ├── getStyles.js │ │ │ │ │ │ ├── isHiddenWithinTree.js │ │ │ │ │ │ ├── rmargin.js │ │ │ │ │ │ ├── rnumnonpx.js │ │ │ │ │ │ └── swap.js │ │ │ │ │ ├── data.js │ │ │ │ │ ├── data │ │ │ │ │ ├── Data.js │ │ │ │ │ └── var │ │ │ │ │ │ ├── acceptData.js │ │ │ │ │ │ ├── dataPriv.js │ │ │ │ │ │ └── dataUser.js │ │ │ │ │ ├── deferred.js │ │ │ │ │ ├── deferred │ │ │ │ │ └── exceptionHook.js │ │ │ │ │ ├── deprecated.js │ │ │ │ │ ├── dimensions.js │ │ │ │ │ ├── effects.js │ │ │ │ │ ├── effects │ │ │ │ │ ├── Tween.js │ │ │ │ │ └── animatedSelector.js │ │ │ │ │ ├── event.js │ │ │ │ │ ├── event │ │ │ │ │ ├── ajax.js │ │ │ │ │ ├── alias.js │ │ │ │ │ ├── focusin.js │ │ │ │ │ ├── support.js │ │ │ │ │ └── trigger.js │ │ │ │ │ ├── exports │ │ │ │ │ ├── amd.js │ │ │ │ │ └── global.js │ │ │ │ │ ├── jquery.js │ │ │ │ │ ├── manipulation.js │ │ │ │ │ ├── manipulation │ │ │ │ │ ├── _evalUrl.js │ │ │ │ │ ├── buildFragment.js │ │ │ │ │ ├── getAll.js │ │ │ │ │ ├── setGlobalEval.js │ │ │ │ │ ├── support.js │ │ │ │ │ ├── var │ │ │ │ │ │ ├── rcheckableType.js │ │ │ │ │ │ ├── rscriptType.js │ │ │ │ │ │ └── rtagName.js │ │ │ │ │ └── wrapMap.js │ │ │ │ │ ├── offset.js │ │ │ │ │ ├── queue.js │ │ │ │ │ ├── queue │ │ │ │ │ └── delay.js │ │ │ │ │ ├── selector-native.js │ │ │ │ │ ├── selector-sizzle.js │ │ │ │ │ ├── selector.js │ │ │ │ │ ├── serialize.js │ │ │ │ │ ├── traversing.js │ │ │ │ │ ├── traversing │ │ │ │ │ ├── findFilter.js │ │ │ │ │ └── var │ │ │ │ │ │ ├── dir.js │ │ │ │ │ │ ├── rneedsContext.js │ │ │ │ │ │ └── siblings.js │ │ │ │ │ ├── var │ │ │ │ │ ├── ObjectFunctionString.js │ │ │ │ │ ├── arr.js │ │ │ │ │ ├── class2type.js │ │ │ │ │ ├── concat.js │ │ │ │ │ ├── document.js │ │ │ │ │ ├── documentElement.js │ │ │ │ │ ├── fnToString.js │ │ │ │ │ ├── getProto.js │ │ │ │ │ ├── hasOwn.js │ │ │ │ │ ├── indexOf.js │ │ │ │ │ ├── pnum.js │ │ │ │ │ ├── push.js │ │ │ │ │ ├── rcssNum.js │ │ │ │ │ ├── rnothtmlwhite.js │ │ │ │ │ ├── slice.js │ │ │ │ │ ├── support.js │ │ │ │ │ └── toString.js │ │ │ │ │ └── wrap.js │ │ │ ├── requirejs │ │ │ │ ├── .bower.json │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ └── require.js │ │ │ └── svg-pan-zoom │ │ │ │ ├── .bower.json │ │ │ │ ├── ISSUE_TEMPLATE.md │ │ │ │ ├── LICENSE │ │ │ │ ├── README.md │ │ │ │ ├── bower.json │ │ │ │ ├── demo │ │ │ │ ├── Tux.svg │ │ │ │ ├── custom-controls.html │ │ │ │ ├── custom-event-handlers.html │ │ │ │ ├── dynamic-load.html │ │ │ │ ├── embed.html │ │ │ │ ├── hammer.js │ │ │ │ ├── img.html │ │ │ │ ├── inline-viewbox-zoomed.html │ │ │ │ ├── inline-wide.html │ │ │ │ ├── inline.html │ │ │ │ ├── jquery.min.js │ │ │ │ ├── layers.html │ │ │ │ ├── limit-pan.html │ │ │ │ ├── mobile.html │ │ │ │ ├── multi-instance.html │ │ │ │ ├── object.html │ │ │ │ ├── pathway.svg │ │ │ │ ├── require-main.js │ │ │ │ ├── require.html │ │ │ │ ├── resize.html │ │ │ │ ├── simple-animation.html │ │ │ │ ├── sinchronized.html │ │ │ │ ├── thumbnailViewer.html │ │ │ │ ├── thumbnailViewer.js │ │ │ │ ├── tiger.svg │ │ │ │ └── wikipathways.html │ │ │ │ ├── dist │ │ │ │ ├── svg-pan-zoom.d.ts │ │ │ │ ├── svg-pan-zoom.js │ │ │ │ └── svg-pan-zoom.min.js │ │ │ │ ├── gulpfile.js │ │ │ │ ├── index.html │ │ │ │ ├── package.json │ │ │ │ ├── server.js │ │ │ │ ├── src │ │ │ │ ├── browserify.js │ │ │ │ ├── control-icons.js │ │ │ │ ├── media │ │ │ │ │ ├── reset.ai │ │ │ │ │ └── reset.svg │ │ │ │ ├── shadow-viewport.js │ │ │ │ ├── stand-alone.js │ │ │ │ ├── svg-pan-zoom.js │ │ │ │ ├── svg-utilities.js │ │ │ │ ├── uniwheel.js │ │ │ │ └── utilities.js │ │ │ │ ├── svg-pan-zoom-logo.png │ │ │ │ ├── svg-pan-zoom-logo.svg │ │ │ │ └── tsconfig.json │ │ ├── css │ │ │ └── main-20180518.css │ │ ├── img │ │ │ ├── BioExcel_logo_cropped.svg │ │ │ ├── CWL-Logo-Header.png │ │ │ ├── CWL-Logo-nofonts.svg │ │ │ ├── Docker-logo.png │ │ │ ├── Flag_of_Europe.svg │ │ │ ├── GitHub-Mark-32px.png │ │ │ ├── children-logo.svg │ │ │ ├── cross.svg │ │ │ ├── gitlogo.png │ │ │ ├── hpc4ai-logo.webp │ │ │ ├── loading.svg │ │ │ ├── manchester.svg │ │ │ ├── parents-logo.svg │ │ │ ├── tick.svg │ │ │ └── workflow-compile.svg │ │ └── js │ │ │ ├── docs.js │ │ │ ├── loading.js │ │ │ ├── main.js │ │ │ ├── selectworkflow.js │ │ │ └── workflow.js │ │ └── templates │ │ ├── about.html │ │ ├── apidocs.html │ │ ├── error │ │ ├── 404.html │ │ └── 5xx.html │ │ ├── fragments │ │ ├── error.html │ │ ├── footer.html │ │ ├── header.html │ │ └── pagination.html │ │ ├── index.html │ │ ├── loading.html │ │ ├── selectworkflow.html │ │ ├── workflow.html │ │ └── workflows.html └── test │ ├── java │ └── org │ │ └── commonwl │ │ └── view │ │ ├── CwlViewerApplicationTests.java │ │ ├── PageControllerTest.java │ │ ├── cwl │ │ ├── CWLElementTest.java │ │ ├── CWLProcessTest.java │ │ ├── CWLServiceTest.java │ │ └── RDFServiceTest.java │ │ ├── docker │ │ └── DockerServiceTest.java │ │ ├── git │ │ ├── GitDetailsTest.java │ │ ├── GitSemaphoreTest.java │ │ └── GitServiceTest.java │ │ ├── graphviz │ │ ├── GraphVizServiceTest.java │ │ └── ModelDotWriterTest.java │ │ ├── researchobject │ │ ├── HashableAgentTest.java │ │ ├── ROBundleFactoryTest.java │ │ └── ROBundleServiceTest.java │ │ ├── util │ │ └── FileUtilsTest.java │ │ └── workflow │ │ ├── PostgreSQLContextInitializer.java │ │ ├── QueuedWorkflowRepositoryTest.java │ │ ├── WorkflowControllerTest.java │ │ ├── WorkflowFormTest.java │ │ ├── WorkflowFormValidatorTest.java │ │ ├── WorkflowJSONControllerTest.java │ │ ├── WorkflowPermalinkControllerTest.java │ │ ├── WorkflowRepositoryTest.java │ │ └── WorkflowServiceTest.java │ └── resources │ ├── cwl │ ├── complex-workflow │ │ └── complex-workflow-1.cwl │ ├── hello │ │ ├── README.md │ │ ├── hello-param.cwl │ │ ├── hello.cwl │ │ ├── hello_doclist.cwl │ │ └── params.json │ ├── licenses │ │ ├── apache │ │ │ └── LICENSE │ │ ├── multiple │ │ │ ├── LICENSE │ │ │ └── LICENSE.MIT │ │ ├── none │ │ │ └── .gitkeep │ │ └── other │ │ │ └── LICENSE │ ├── lobstr-draft3 │ │ ├── README │ │ ├── allelotype.cwl │ │ ├── lobSTR-arvados-demo.json │ │ ├── lobSTR-demo.json │ │ ├── lobSTR-tool.cwl │ │ ├── lobSTR-workflow.cwl │ │ ├── models │ │ │ ├── illumina_v3.pcrfree.stepmodel │ │ │ └── illumina_v3.pcrfree.stuttermodel │ │ ├── samtools-index.cwl │ │ ├── samtools-sort.cwl │ │ ├── tmp_1.fq │ │ └── tmp_2.fq │ ├── lobstr-v1 │ │ ├── README │ │ ├── allelotype.cwl │ │ ├── lobSTR-arvados-demo.json │ │ ├── lobSTR-demo.json │ │ ├── lobSTR-tool.cwl │ │ ├── lobSTR-workflow.cwl │ │ ├── models │ │ │ ├── illumina_v3.pcrfree.stepmodel │ │ │ └── illumina_v3.pcrfree.stuttermodel │ │ ├── samtools-index.cwl │ │ ├── samtools-sort.cwl │ │ ├── tmp_1.fq │ │ └── tmp_2.fq │ ├── make_to_cwl │ │ ├── Makefile │ │ ├── README.md │ │ ├── dna.cwl │ │ ├── dna.ttl │ │ ├── rna.json │ │ └── visualisation.dot │ ├── nested_array.cwl │ ├── null_default.cwl │ └── oneline_optional_types.cwl │ ├── graphviz │ ├── testVis.png │ ├── testVis.svg │ └── testWorkflow.dot │ └── it-application.properties └── start-jena.sh /.git-blame-ignore-revs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/common-workflow-language/cwlviewer/HEAD/.git-blame-ignore-revs -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/common-workflow-language/cwlviewer/HEAD/.github/dependabot.yml 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