Develop => master for AWS-v87 #52
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) * Draft support for optional FileHash * Draft getMd5 for BlobPath * Resolve non-parallel IO to fix tests * Checksum validation for BlobPath * Nicer error message * Test for missing Blob hash * Break attr acquisition into separate method * Cleanup, comments * In-progress tests of blob hash command * Remove test * Remove unused import
* BT-711 Refresh SAS token for filesystem on expiry * Rough cut of token refresh using exceptions * Ignore tests, and minor cleanup * Remove stray line * Draft of manager class for handling expiring file systems * Style fixes * Refactor of blobfilesystemManager and tests covering its functionality * Refined tests to validate close filesystem as separate unit * Ignore connected tests * Clean up of some things * Refactor BlobFileSystemManager to separate file, and some other cleanup * Some additional scala-ifying * Small cleanup * Correcting imports * trigger tests * trigger tests
* Batch 1 of scala steward updates * Rollback snakeYAML * Attempt 3, with only the passing dependancies * Revert google API and Big Query udpates * Winding back other google deps * rollback remaining google updates * trigger tests * trigger tests
* Update SBT to 2.0.0 * Fix sbt-git import * Update mouse to 1.0.11 * Update rhino 1.7.14
* Reorder execution result checks so 137 can retry with more memory * Test for memory retry after 137 RC * Fix test expectations * Make memory retry checks consistent * Revert changes to existing test * Rename retryWithMoreMemory to outOfMemoryDetected
* Scala steward updates batch 3
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
* Give blob SAS tokens write permission * Case class wrapper for subscription id * Resolve duplicate container name in absolute BlobPath * Ignored test demonstrating correct absolute path generation * Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala Co-authored-by: Brian Reilly <breilly@broadinstitute.org> * PR feedback Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
* update snakeyaml to 1.33 * Don't use deprecated no-arg Constructor constructor Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
* Update Scala to 2.13.9 * Try updating sbt-scoverage * Does this version exist anywhere we can see? * This version actually exists * Update library version to remove conflict * Codegen version * Fix fun new 2.13.9 compiler errors * Resolve warnings * Newest Scala? * I guess not * Does this please Travis? * force ci * Back out changes to generated code Co-authored-by: Adam Nichols <aednichols@gmail.com>
…dinstitute#6935) Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1. - [Release notes](https://github.com/FasterXML/jackson/releases) - [Commits](https://github.com/FasterXML/jackson/commits) --- updated-dependencies: - dependency-name: com.fasterxml.jackson.core:jackson-databind dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* `hostAllowlist` that allows everything * Refactor * Stick allow list in HttpResolver * Better default config * Allow list tests * Make it build Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
* Log messages * `DEBUG` -> `INFO`
…nstitute#6941) * Modify blob paths for TES * Make blob transformation configurable * Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala Co-authored-by: Adam Nichols <anichols@broadinstitute.org> * Apply PR feedback in second place Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
* More updated client for use in cbas * Removing excess code
* wx-837 removed cwl references in markdown doc files * wx-837 removed cwlParsingOverview.md, updated mkdocs.yml * wx-837 updated cromwell.yaml, generated new RESTAPI file
* Dependencies * Compiles but no tests * Formatting * Moar exclusions * Update to latest WSM * Add additional dependency * We need some UUID here to make the request * Formatting * Clarify what is fake * Formatting * Use our own version of Jersey and Jackson stuff * Port-in Khalid's changes (thank you!) Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org> * Test longevity Don't break the test if someone decides to add a cert to `ws.org` * Cleanup * Cleanup * Cleanup * Adjust TES config file for CI Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org> Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>
* crom-6554 removed references to PAPI v1 from doc * crom-6554 pr feedback, reworded doc to use example conf as a starting point
Run `sbt -Dproject.isDebug=true server/docker`
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: quekx <quekx@gene.com>
…on of changes on aws_develop branch
…S fixes for now while waiting for feedback
Fix/efs caching
Develop aws
henriqueribeiro
approved these changes
Nov 6, 2024
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merging towards release