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fix: Use constructor injection instead of field injection in Java code in Challenge-Service App #1

Merged
merged 89 commits into from
Sep 8, 2023

Commits on Aug 2, 2023

  1. chore: Remove OpenChallenges MinIO (Sage-Bionetworks#1880)

    * Remove openchallenges-minio
    
    * Remove references to MinIO
    
    * Remove references to MinIO
    tschaffter authored Aug 2, 2023
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  2. fix(ui): remove drop shadows from select cards (Sage-Bionetworks#1905)

    * remove drop shadow from org card
    
    * remove drop shadow from goal card
    
    * add grey border around logo on org card
    vpchung authored Aug 2, 2023
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  3. fix(ui): Add default text for empty fields on profile pages (Sage-Bio…

    …networks#1904)
    
    * add default value for missing DOI
    
    * update name of template
    
    * add default value for empty inputDataTypes
    
    * add default value for empty incentives
    
    * use grey text for "NA" values
    vpchung authored Aug 2, 2023
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  4. chore: Remove OpenChallenges DB CLI (Sage-Bionetworks#1882)

    * Remove OC DB CLI
    
    * Remove references to OC DB CLI
    
    * Remove references to OC DB CLI
    tschaffter authored Aug 2, 2023
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Commits on Aug 3, 2023

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  2. feat: Implement challenge contributors in Challenge Profile (Sage-Bio…

    …networks#1893)
    
    * add angular to get contributions
    
    * change orgId t o string
    
    * replace sponsors with contributors
    
    * update org card component
    
    * update some org card layouts
    
    * not show members by default and update org card layouts
    
    * use `grid` on card-group to better fit our cards layout
    
    * hide members
    
    * fix cards layout in home
    
    * add brief description to profile page sections (#2)
    
    * Update libs/openchallenges/challenge/src/lib/challenge-contributors/challenge-contributors.component.html
    
    Co-authored-by: Thomas Schaffter <[email protected]>
    
    * fix grid space for person cards
    
    * fix org-member's space
    
    ---------
    
    Co-authored-by: Verena Chung <[email protected]>
    Co-authored-by: Thomas Schaffter <[email protected]>
    3 people authored Aug 3, 2023
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  3. feat: Specify the data version in the OC footer (Sage-Bionetworks#1916)

    * Add `Data updated on` to the footer
    
    * Update config for container
    tschaffter authored Aug 3, 2023
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  4. feat(ui): Modify the default organization sorting to be based on the …

    …`challenge_count` (Sage-Bionetworks#1910)
    
    * change default sort to challenge_count in org search
    
    * sort orgs in challenge contributors
    
    * sort by alphabetic in challenge-contributors
    rrchai authored Aug 3, 2023
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  5. feat(ui): Open and reorder challenge filters (Sage-Bionetworks#1908)

    * reorder filters for challenges
    
    * open all filters for challenges
    
    * comment out input data type filter
    
    * move year down
    
    * add back input data type and put dropdowns together
    
    * move input data type up
    
    * hide input data type filter
    rrchai authored Aug 3, 2023
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  6. feat(ui): Hide user related widgets across app (Sage-Bionetworks#1915)

    * diable user direction
    
    * hide challenge-stargazers
    
    * hide user metrics in home
    
    * hide star button on cards
    rrchai authored Aug 3, 2023
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  7. docs: Update the Team page (Sage-Bionetworks#1919)

    * Limit to 3 members per row
    
    * Add link to profiles
    
    * Add LinkedIn icon for maria but wo url for now
    
    * Make .card-roles use all its space
    
    * Fix width of the roles instead of using br
    
    * Pack together the members and add bmargin below team
    
    * Update libs/openchallenges/team/src/lib/team.component.html
    
    Co-authored-by: Verena Chung <[email protected]>
    
    * RRemove maria Linkedin
    
    ---------
    
    Co-authored-by: Verena Chung <[email protected]>
    tschaffter and vpchung authored Aug 3, 2023
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  8. feat(ui): Make width of challenge and org cards consistent (Sage-Bion…

    …etworks#1921)
    
    * make width of challenge and org cards consistent
    
    * fix failed test on org-card
    
    * remove row col in parent tag of car-group
    rrchai authored Aug 3, 2023
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Commits on Aug 4, 2023

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  4. feat: Add ACM certificate for OC prod DNS (Sage-Bionetworks#1925)

    * Add prod cert
    
    * Fix typo
    
    * Keep a single cert
    
    * Undo changes
    
    * More undo
    
    * Fix stack after forgetting initial cert
    tschaffter authored Aug 4, 2023
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  8. feat: Setup Google Analytics (Sage-Bionetworks#1923)

    * Add Tag Manager code to header
    
    * Add Google Tag Manager
    
    * Remove GTM from index.html
    
    * Send GTM tag when loading a page
    
    * Send tag when viewing a page
    tschaffter authored Aug 4, 2023
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  9. chore: Point openchallenges.io to the OC preview EC2 instance (Sage…

    …-Bionetworks#1941)
    
    * Use new cert with the preview instance ALB
    
    * Add new DNS record
    tschaffter authored Aug 4, 2023
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Commits on Aug 5, 2023

  1. feat(ui): Add announcement box in the home page (Sage-Bionetworks#1939)

    * add blank text
    
    * add some colors
    
    * adjust spacing a bit
    
    * Update libs/openchallenges/home/src/lib/home.component.html
    
    Co-authored-by: Verena Chung <[email protected]>
    
    * Update libs/openchallenges/home/src/lib/home.component.html
    
    Co-authored-by: Thomas Schaffter <[email protected]>
    
    * update some texts
    
    * adjust color using amber50&500
    
    * fix typo
    
    * Update libs/openchallenges/home/src/lib/home.component.html
    
    Co-authored-by: Verena Chung <[email protected]>
    
    * remove redirection link to about page
    
    ---------
    
    Co-authored-by: Verena Chung <[email protected]>
    Co-authored-by: Thomas Schaffter <[email protected]>
    3 people authored Aug 5, 2023
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  3. feat(ui): Adjust layout of cards (Sage-Bionetworks#1932)

    * replace auto-fit by auto-fill
    
    * remove justify-items in home since not needed anymore
    
    * add media for card-group
    
    * update spacing for person card
    
    * change to use fixed width for cards
    
    * use 320px back for card width
    
    * align center for cards in home
    
    * change back to 300px since limited space in search page
    rrchai authored Aug 5, 2023
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  5. fix(ui): Hide in-progess items for soft launch (Sage-Bionetworks#1944)

    * hide stargazers metric
    
    * show N number of views
    
    * hide verfication badge for now
    vpchung authored Aug 5, 2023
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Commits on Aug 14, 2023

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  2. feat(data): weekly OC db update (Sage-Bionetworks#1952)

    * daily update; add 1 new challenge
    
    * daly update; add 3 new orgs
    
    * update challenge headlines and descriptions
    
    * add new platform
    
    * add new challenges
    
    * update org desc
    
    * add new orgs
    
    * add platform for "other"
    
    * update associating platform IDs
    
    * add 3 challenges
    
    * add 8 orgs; update challenge counts
    
    * fix: add "" to enum of status values
    
    * revert 594b45b "fix" ('twas not a fix...)
    
    * give "Other" platform id of 0
    
    * reassign og platform ids; assign statuses to empty ones
    
    * assign id=14 for "Other" platform
    
    * add 2 challenges
    
    * add 6 orgs
    
    * Add Eterna logo
    
    * Update app data last updated on
    
    * Update app data last updated on
    
    ---------
    
    Co-authored-by: Thomas Schaffter <[email protected]>
    vpchung and tschaffter authored Aug 14, 2023
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  3. feat: Add /components/{componentLabel}/attributes endpoint (Sage-Bion…

    …etworks#1903)
    
    * add endpoint
    
    * filled in docstrings
    
    * fix backward arguments
    
    * moved schemaUrl from path to query folder
    
    * fix c+p error
    
    * handle merge conflict
    
    * fix typo
    andrewelamb authored Aug 14, 2023
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  4. chore(ng): Migrate the project openchallenges-challenge to Ng stand…

    …alone components (Sage-Bionetworks#1957)
    
    * Convert challenge-contributor to standalone
    
    * Convert challenge-organizers to standalone
    
    * Convert all components to standalone
    
    * Finalize challenge project
    tschaffter authored Aug 14, 2023
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  5. chore(ng): Migrate the project openchallenges-home and `openchallen…

    …ges-challenge-search` to Ng standalone components (Sage-Bionetworks#1959)
    
    * Migrate challenge-search lib to standalone
    
    * Migrate ng config lib
    
    * Migrate home challenge search component
    
    * Finalize migration to standalone components
    
    * Fix test
    tschaffter authored Aug 14, 2023
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  6. chore(ng): Migrate projects to ng standalone components (Part 3) (Sag…

    …e-Bionetworks#1961)
    
    * Migrate openchallenges-login to standalone components
    
    * Migrate openchallenges-not-found to standalone components
    
    * Migrate openchallenges-signup
    
    * Migrate openchallenges-team
    
    * Migrate openchallenges-util
    
    * Migrate openchallenges-user-profile
    
    * Migrate openchallenges-org-profile
    
    * Migrate openchallenges-org-search
    tschaffter authored Aug 14, 2023
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Commits on Aug 15, 2023

  1. chore(ng): Migrate the project openchallenges-ui to Ng standalone c…

    …omponents (Sage-Bionetworks#1964)
    
    * Migrate some components from ui
    
    * Fix tests
    
    * Remove imports of UiModule
    
    * Remove UiModule
    tschaffter authored Aug 15, 2023
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Commits on Aug 16, 2023

  1. chore(ng): Migrate to Ng self-closing tags (Sage-Bionetworks#1973)

    * Use Ng self-closing tags
    
    * Remove remaining references to UiModule
    tschaffter authored Aug 16, 2023
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Commits on Aug 17, 2023

  1. feat: Investigate yarn cache folder (Sage-Bionetworks#1979)

    * Investigate yarn cache folder
    
    * Mount yarn cache folder
    
    * ls cache folder in container
    
    * Install yarn packages
    
    * Install Yarn packages without the cache
    
    * Install Yarn packages without the cache
    
    * Reenable caching
    
    * Cleanup
    
    * Update workflow that runs when pushing to main
    
    * Restore docker-outside-of-docker
    
    * Use more robust path to yarn cache
    
    * Comment out poetry to trigger new run
    tschaffter authored Aug 17, 2023
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Commits on Aug 18, 2023

  1. feat: Cache R packages in CI workflow (Sage-Bionetworks#1982)

    * Set up renv cache
    
    * Mount R cache folder
    
    * Create cache folder
    
    * Prefix with yarn
    
    * chmod
    
    * sudo
    
    * ls
    
    * chown again
    
    * sudo again
    
    * prepare-r
    
    * Reorder
    
    * Install node.js packages
    
    * fix typo
    
    * Trigger new run
    
    * Try to force update
    
    * trigger
    
    * trigger
    
    * Cleanup
    tschaffter authored Aug 18, 2023
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  3. feat: Add /nodes/{nodeLabel}/dependencies endpoint (Sage-Bionetworks#…

    …1913)
    
    * add endpoint
    
    * filled in docstrings
    
    * fix backward arguments
    
    * moved schemaUrl from path to query folder
    
    * add new endpoint
    
    * add new endpoint
    
    * fix c+p error
    
    * fx c+p error
    
    * change endpoint operationId
    
    * change endpoint operationId
    
    * handle merge conflict
    
    * change name of endpoint
    
    * fix docstring terminology
    andrewelamb authored Aug 18, 2023
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  4. feat: Cache Poetry and venv in CI workflow (Sage-Bionetworks#1983)

    * Cache Poetry and venv
    
    * Install Node.js packages
    
    * trigger
    
    * Debug
    
    * Debug
    
    * Debug
    
    * Dub
    
    * Remove single quotes
    
    * Trigger
    
    * Without cache (reference)
    
    * Restore poetry cache
    
    * Caching venv
    
    * Cleanup
    
    * Cleanup
    tschaffter authored Aug 18, 2023
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  5. feat: Cache Gradle in CI workflow (Sage-Bionetworks#1988)

    * Prepare caching for Gradle
    
    * Fix missing mount in CI workflow for main
    
    * Fix typo
    
    * Cleanup
    
    * Trigger
    
    * Undo trigger
    tschaffter authored Aug 18, 2023
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Commits on Aug 19, 2023

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  3. fix: Update dev-env.sh

    tschaffter authored Aug 19, 2023
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  4. chore: Migrate the project openchallenges-app to Ng standalone compon…

    …ents (Sage-Bionetworks#1993)
    
    * Migrate remaining components to Ng standalone
    
    * Migrate app to standalone
    tschaffter authored Aug 19, 2023
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Commits on Aug 21, 2023

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  3. chore(tools): Add SonarScanner CLI to the devcontainer (Sage-Bionetwo…

    …rks#2000)
    
    * Add pnpm to the devcontainer
    
    * Add SonarScanner CLI to the devcontainer
    tschaffter authored Aug 21, 2023
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Commits on Aug 22, 2023

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Commits on Aug 23, 2023

  1. feat(ui): Adjust long texts to better fit on challenge card (Sage-Bio…

    …networks#1987)
    
    * change back to use 320px width for cards
    
    * increase title height
    
    * Revert "increase title height"
    
    This reverts commit eddf362.
    
    * Revert "change back to use 320px width for cards"
    
    This reverts commit d685159.
    
    * change back to use 320px width for cards
    
    * match title height with line height
    
    * truncate title to 60 characters
    
    * Revert "change back to use 320px width for cards"
    
    This reverts commit facb213.
    
    * avoid breaking words
    
    * exclude special characters
    
    * use css approach to truncate long texts
    
    * remove extra space
    
    * improve footer layout
    
    * change width back to 320px on cards
    
    * remove height for footer
    
    * adjust card group layout
    
    * Revert "adjust card group layout"
    
    This reverts commit 1d7afea.
    
    * update min-height
    
    * change variable name in line-camp mixin
    
    * rename mixin
    
    * fix typo
    rrchai authored Aug 23, 2023
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Commits on Aug 24, 2023

  1. feat: add /nodes/{nodeLabel}/validationRules endpoint (Sage-Bionetwor…

    …ks#1918)
    
    * add endpoint
    
    * filled in docstrings
    
    * fix backward arguments
    
    * moved schemaUrl from path to query folder
    
    * add new endpoint
    
    * add new endpoint
    
    * fix c+p error
    
    * fx c+p error
    
    * change endpoint operationId
    
    * change endpoint operationId
    
    * add new endpoint
    
    * add new endpoint
    
    * add component Display
    
    * add component Display
    
    * add component Display
    
    * handle merge conflict
    
    * add new endpoint
    
    * handle merge
    
    * change name of endpoint
    
    * chnage diescription of validation rule
    andrewelamb authored Aug 24, 2023
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Commits on Aug 25, 2023

  1. fix: Fix CI workflow access to Yarn cache folder (Sage-Bionetworks#2012)

    * Disable Yarn cache
    
    * Print .yarn/cache
    
    * Update perm yarn cache
    
    * Create yarn cache folder if it does not exist
    
    * More robust method
    
    * Fix typo
    
    * Update root permission
    
    * Update workflow for main
    
    * Cleanup
    
    * Set up buildx
    
    * Switch back to did
    
    * Switch back to did
    
    * Update did to 2.3.1
    
    * No longer mount docker
    
    * Cleanup
    
    * Update to dev container CLI  0.51.0
    
    * Undo last commit
    
    * Back to did 20.10.24
    tschaffter authored Aug 25, 2023
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  4. feat: Change endpoint names to use nodes instead of components (Sage-…

    …Bionetworks#1977)
    
    * add endpoint
    
    * filled in docstrings
    
    * fix backward arguments
    
    * moved schemaUrl from path to query folder
    
    * add new endpoint
    
    * add new endpoint
    
    * fix c+p error
    
    * fx c+p error
    
    * change endpoint operationId
    
    * change endpoint operationId
    
    * add new endpoint
    
    * add new endpoint
    
    * add component Display
    
    * add component Display
    
    * add component Display
    
    * handle merge conflict
    
    * add new endpoint
    
    * handle merge
    
    * change name of endpoint
    
    * rename endpoints
    
    * chnage diescription of validation rule
    
    * change endpoint name
    
    * change endpoint name
    
    * change endpoint name
    
    * update pythn version
    
    * update pythn version
    
    * fix unintentional change
    andrewelamb authored Aug 25, 2023
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Commits on Aug 27, 2023

  1. chore: Update Dev Container CLI (Sage-Bionetworks#2024)

    * Update Dev Container CLI
    
    * Update Trivy
    
    * Update most tools
    
    * Restore devcontainer CLI 0.50.2
    tschaffter authored Aug 27, 2023
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Commits on Aug 28, 2023

  1. feat: Notify Developers when they need to update VS Code (Sage-Bionet…

    …works#2010)
    
    * Invite to update vs code
    
    * Cleanup
    
    * Add dot
    
    * Update message
    
    * Make message more user friendly
    tschaffter authored Aug 28, 2023
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Commits on Aug 29, 2023

  1. feat: Navigate to search pages when clicking on the home page stats (S…

    …age-Bionetworks#2020)
    
    * Make stats clickable
    
    * Add RouterTestingModule to unit test
    
    * Fix home tests
    tschaffter authored Aug 29, 2023
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  3. feat: Generate and publish coverage report for one Java project (Sage…

    …-Bionetworks#2032)
    
    * Configure sonar for OC image service
    
    * Add JaCoCo
    
    * Run jacoco as part of the test task
    
    * Remove gradlew.bat
    
    * Add task `sonar`
    
    * Minor improvement
    
    * Add badges to image-service
    tschaffter authored Aug 29, 2023
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  5. feat: Add /assetTypes/{assetType}/assetViews/{assetViewId}/datasets/{…

    …datasetId}/files endpoint (Sage-Bionetworks#2026)
    
    * add new endpoint
    
    * revert unintentional change
    andrewelamb authored Aug 29, 2023
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  7. ci: Push Sonar scan results when pushing to main (Sage-Bionetworks#…

    …2043)
    
    * Pass SONAR_TOKEN to dev container
    
    * Run sonar when merging to `main` in CI workflow
    tschaffter authored Aug 29, 2023
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Commits on Aug 30, 2023

  1. chore(java): Upgrade to Gradle v8 (Sage-Bionetworks#2050)

    * Update the image service to use gradle v8
    
    * Update the image service to use gradle v8
    
    * Update the challenge service
    
    * Update the organization service
    
    * Update the apu gateway
    
    * Update the auth-service
    
    * Update challenge-to-elasticsearch-service
    
    * Update config-server
    
    * Update core-service
    
    * Update kaggle-to-kafka-service
    
    * Update service-registry
    
    * Update user-service
    
    * Update app-config-data
    
    * Update kafka-admin
    
    * Update kafka-consumer
    
    * Update kafka-model
    
    * Update kafka-producer
    
    * Update shared-java-util
    tschaffter authored Aug 30, 2023
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  2. feat: Scan OC Angular app with Sonar (Sage-Bionetworks#2052)

    * Add sonar scanner tool
    
    * Validate args
    
    * Define sonar task for openchallenges-app
    tschaffter authored Aug 30, 2023
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  3. ci: Scan Schematic API with Sonar (Sage-Bionetworks#2054)

    * Simplify the syntax of the `sonar` task
    
    * Update the sonar task of openchallenges-app
    
    * Fix doc
    tschaffter authored Aug 30, 2023
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Commits on Sep 1, 2023

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Commits on Sep 2, 2023

  1. docs: Create dashboard to track code quality (Sage-Bionetworks#2056)

    * Create CODE_QUALITY.md
    
    * Add more projects
    
    * Use bold font for product name
    
    * Add data for OC organization service
    
    * Add metrics for OC challenge service
    
    * Add Section Definitions
    tschaffter authored Sep 2, 2023
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Commits on Sep 4, 2023

  1. refactor: Rename the task prepare to create-config (Sage-Bionetwo…

    …rks#2076)
    
    * Remove `shx`
    
    * Rename task `prepare` to `create-config`
    tschaffter authored Sep 4, 2023
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Commits on Sep 5, 2023

  1. chore: Update OC image service to OpenAPI Generator v7 (Sage-Bionetwo…

    …rks#2079)
    
    * Update OpenAPI Generator to v7
    
    * Regenerate image service
    
    * Run OpenAPI Generator and fixes issues
    
    * Update tool
    tschaffter authored Sep 5, 2023
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  2. refactor: Deprecate tasks prepare-<languages> (Sage-Bionetworks#2083)

    * Define prepare task for R projects
    
    * Small improvement
    
    * Define prepare task for Java projects
    
    * Define prepare task for Python projects
    
    * Update command `workspace-install`
    tschaffter authored Sep 5, 2023
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Commits on Sep 6, 2023

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  2. ci: Add the command workspace-install-affected (Sage-Bionetworks#2089)

    * Add the command `workspace-install-affected`
    
    * Use new command in CI workflow
    tschaffter authored Sep 6, 2023
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  3. chore: Update the Dev Container August 2023 (Sage-Bionetworks#2025)

    * Restore changes made in Sage-Bionetworks#2023
    
    * Remove 2 deprecated workflow
    
    * Add VS Code extension `github.vscode-github-actions`
    
    * Add VS Code extension `ms-playwright.playwright`
    tschaffter authored Sep 6, 2023
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Commits on Sep 7, 2023

  1. update index.build

    mdsage1 committed Sep 7, 2023
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  4. update SecurityCOnfiguration

    mdsage1 committed Sep 7, 2023
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  5. last files updated

    mdsage1 committed Sep 7, 2023
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  6. update final files

    mdsage1 committed Sep 7, 2023
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Commits on Sep 8, 2023

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  2. update typo

    mdsage1 committed Sep 8, 2023
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