cwlviewer v1.4: catch up since 2018, includes fix for CVE-2021-41110

Many updates since 2018, but the most important is the fix (#355) for CVE-2021-41110 courtesy of @kinow

New features:

• Streamable CWL graph images #240 @stain
• Schedule recurrent CWL Viewer maintained cron-job for purging of old queued workflows from database #326 @obasekiosa

Smaller changes:

• Separate workflow URL from repository URL in "retrieved from" column of workflows page #316 @obasekiosa
• Fix replace non working deleteByRetrievedFrom function with working delete function #321 @obasekiosa

Documentation updates:

• Update README.md to explain better how to get started #308 @Anushka-shukla
• README.d: correct example URL to use port 8080 #311 @yichiehc
• Add links to the 2017 Video overview & Mark's report 612f5b4 b83b4fd 3380d44 @mr-c @stain
• Notes on running Mongo/Jena in Docker, and spring boot on host #334 @tetron
• Typos in README.md #349 @kinow

Misc fixes:

• Update jena & switch to Turtle syntax for SPARQL connection #213 @stain
• fix reversed class & id attributes #235 @mr-c & fixed by @kinow in #352 #353
• Use HTTPS instead of HTTP to resolve dependencies #250 [security update!] @JLLeitschuh
• Indexing retrievedOn in mongo to fix "Clicking 'Last' on the Explore page gives ISE" (#270) 922b434 @stain
• Update copyright year (#286) @stain
• add skip-schemas to the cwltool invocation so we are more lenient

Changes related to the migration of view.commonwl.org from University of Manchester to Curii, Inc (Many thanks to @stain and UNIMAN for their years of service to the public!)

• Add restart:always in docker-compose.yml #294 @cure
• Update the data controller for the https://view.commonwl.org instance. #297 @cure
• Tweaks for the docker-compose.yml file & set a larger internalQueryExecMaxBlockingSortBytes value for mongod #298 @cure
• Remove mention of dev instance 51a7d38 @tetron

Dependencies upgrade:

• Dependency upgrades to patch security vulnerabilities in transitive dependencies (Fixes CVE-2017-5929 CVE-2018-7489 CVE-2017-7525 CVE-2017-15095 CVE-2017-17485 CVE-2018-5968 CVE-2017-5651 CVE-2016-3093 CVE-2017-5648 CVE-2017-5650 CVE-2017-5647) #209 @MarkRobbo
• More dependency upgrades via @snyk-bot #223 #225 #289 #342
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHETHRIFT-173706
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHETOMCATEMBED-451342
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHETOMCATEMBED-451343
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHETOMCATEMBED-451458
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHETOMCATEMBED-451459
  • https://snyk.io/vuln/SNYK-JAVA-ORGAPACHECOMMONS-460507
  • https://snyk.io/vuln/SNYK-RUBY-FFI-22037
  • https://snyk.io/vuln/SNYK-RUBY-JEKYLL-451462
  • https://snyk.io/vuln/SNYK-RUBY-KRAMDOWN-585939
  • https://snyk.io/vuln/SNYK-RUBY-ADDRESSABLE-1316242
  • https://snyk.io/vuln/SNYK-RUBY-KRAMDOWN-1087436
  • https://snyk.io/vuln/SNYK-RUBY-REXML-1244518
• Even more dependency updates, courtesy of @dependabot-preview
  • Bump snakeyaml from 1.23 to 1.29 #233 #253 #276 #300 #340
  • Bump jsonld-java from 0.12.1 to 0.13.3 #232 #242 #277 #315
  • Bump jackson-core from 2.9.6 to 2.12.5 #229 #238 #246 #256 #267 #272 #278 #317 #241 #346
  • Bump org.eclipse.jgit from 4.9.7.201810191756-r to 5.11.0.202103091610-r #230 #245 #251 #258 #259 #266 #271 #275#302
  • Bump jena-osgi from 3.11.0 to 4.1.0 #237 #248 #264 #269 #309 #338
  • Bump commons-compress from 1.19 to 1.21 #330 #343
• spring-boot 1.5.22 @mr-c ea1e273

CI updates:

• stop double testing PRs with Travis (#234) @mr-c
• speed up Travis by caching maven ea47b4a @mr-c
• Install codeql-analysis.yml #268 @mr-c (this helped @kinow and I find CVE-2021-41110; thanks https://github.com/github/codeql-action !)
• Update primary branch name to main 3e3865c @mr-c
• Mergify: configuration update a867bd3 1178ed2 @mr-c
• Upgrade to GitHub-native Dependabot 0a5b427 @mr-c
• Update codeql-analysis.yml to run less often 50401a5 @mr-c
• codeql: git checkout HEAD^2 is no longer necessary 2502986 @mr-c