WM-2296: Callback should supply fully qualified output names #7234
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jgainerdewar
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salonishah11
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* BT-732 Checksum validation for blobs read by engine (broadinstitute#6838) * 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 (broadinstitute#6831) * 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 (broadinstitute#6903) * 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 * [BW-1398] Migrate PKs to BIGINT (broadinstitute#6907) * BT-745 Batch 2 of scala steward updates (broadinstitute#6906) * Update SBT to 2.0.0 * Fix sbt-git import * Update mouse to 1.0.11 * Update rhino 1.7.14 * SUP-692 Retry with more memory after RC 137 (broadinstitute#6912) * 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 (broadinstitute#6913) * Scala steward updates batch 3 * WX-745 Batch 4 scala steward updates (broadinstitute#6916) * WX-746 Localize all DRS inputs in a single Action (broadinstitute#6914) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-755 Build all images instead of just Cromwell (broadinstitute#6919) * WX-755 Add `isRelease` option for Docker builds (broadinstitute#6923) * WX-755 Cromwell/CromIAM automatically board train (broadinstitute#6924) * WX-755 Fix environment variable syntax (broadinstitute#6926) * WX-743 Enable TES task creation with BlobPaths (broadinstitute#6921) * 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 <[email protected]> * PR feedback Co-authored-by: Brian Reilly <[email protected]> * [WX-765] Update snakeyaml to 1.33 (broadinstitute#6927) * update snakeyaml to 1.33 * Don't use deprecated no-arg Constructor constructor Co-authored-by: Janet Gainer-Dewar <[email protected]> * WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (broadinstitute#6925) * Upgrade Postgres to 42.4.1 (broadinstitute#6932) * WX-735 Fix incorrect and/or nondeterministic filesystem ordering (broadinstitute#6930) * WX-772 Update Scala to 2.13.9 (broadinstitute#6928) * 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 <[email protected]> * WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (broadinstitute#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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * WX-808 Host allowlist for HTTP imports (broadinstitute#6938) * `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 <[email protected]> * Update commons text to 1.10.0 (broadinstitute#6937) * WX-751 Token refresh signal for monitoring (broadinstitute#6939) * Log messages * `DEBUG` -> `INFO` * WX-744 Optionally rewrite blob paths to appear as local paths (broadinstitute#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 <[email protected]> * Apply PR feedback in second place Co-authored-by: Adam Nichols <[email protected]> * Update changelog for wdl http allow list (broadinstitute#6944) * WM-1491 Fixing Cromwell-client (broadinstitute#6943) * More updated client for use in cbas * Removing excess code * Fix client build script (broadinstitute#6945) * WX-837: Remove CWL references from documentation (broadinstitute#6949) * 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 * WX-728 Add configurable WSM client to Cromwell (broadinstitute#6948) * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Khalid Shakir <[email protected]> * CROM-6554: Removed PAPIv1 references from doc (broadinstitute#6950) * crom-6554 removed references to PAPI v1 from doc * crom-6554 pr feedback, reworded doc to use example conf as a starting point * WX-833 Real Azure DRS Credentials (broadinstitute#6952) * Remove B2C reference from name * Get token for current user rather than getting from KeyVault * Remove KeyVault config for engine * Remove KeyVault config for DRSLocalizer * Remove KeyVault dependency * Remove KeyVault support from localizer repo template * Cleaned up and working Azure token acquisition for engine * Collapse localizer's AccessTokenStrategy into DrsCredentials * Cleanup * WX-853 Remove most CWL (broadinstitute#6955) * WX-696 Enable getting SAS token from WSM (broadinstitute#6954) * WX-696 Enable getting SAS token from WSM * Wire container resource id from config * Move resource-container-id config path * First pass at config for WSM * Remove unused singleton config * Tests for new config * Fix config parsing * Modified b2c token to be provided each time * Remove singletonConfig arg from factory * Restore types to factory configs * Clean up comments and empty token default * Default to config b2c before searching environment * Fix token default on api client * Fix test * Refactor error handling for when there is no token * Remove token constructor arg for clientProvider * Move configs to global singleton config * Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala * default -> override * Add override token to test * Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala Co-authored-by: Adam Nichols <[email protected]> * Parentheses * Reduce token timeout * Move AzureCredentials to separate file * Make AzureCredentials an object * WSM token cleanup * Config refactor (broadinstitute#6960) Co-authored-by: Janet Gainer-Dewar <[email protected]> * Initial blob token documentation * Refine language in BlobSasTokenGenerator * Update comment and formatting Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * WX-853 Remove CWL language factory, Centaur runner (broadinstitute#6961) * WX-842 Add Pact Dependency for Cromwell (broadinstitute#6962) * WX-842 Add Pact Dependency for Cromwell * Remove incomplete test spec * Initial Pact Test * Fix pact so it compiles * Add breadcrumb comment and clean up * ID-125 Add support for drshub, rename all the things (broadinstitute#6959) * Add support for drshub, rename all the things * fallback to martha if resolver is not in config * WX-867 Translate crc32c hashes to b64 for getm (broadinstitute#6970) * Translate crc32c hashes to b64 for getm * Update tests * Remove obsolete b64 handling for md5, centralize hex validation * Restore old test, fix other test * WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (broadinstitute#6965) * WX-859 Accept workflow execution identity in config (broadinstitute#6967) * WX-892 Trim down `ValueStore` logging to prevent OOMs (broadinstitute#6981) * Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (broadinstitute#6975) * WX-863 Turn off Azure NIO logging (broadinstitute#6982) * Turn off Azure NIO logging * Poke Travis * WM-1616: Allow repeating attempts at initialization (take 2) (broadinstitute#6985) * WX-878 Single shared BlobFileSystemManager (broadinstitute#6986) * Make BlobFileSystemManager shared across all BlobPathBuilders * Update TES conf file to reflect new singleton config * Shell escape reference image files [VS-796] [WX-910] (broadinstitute#6989) * WX-769 `disks` compatibility for TES backend (broadinstitute#6991) * Update FiveMinuteIntro.md (broadinstitute#6994) * WX-906 Sbt Unit Tests as Github Actions (broadinstitute#6992) * WX-926 Support falling back to OCI Manifest Format (broadinstitute#7003) * WX-926 Support falling back to OCI Manifest Forma * Only mount reference disks if requested [WX-925] (broadinstitute#7001) * [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (broadinstitute#7004) * WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (broadinstitute#6980) * WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status * Address feedback * Address feedback (broadinstitute#6997) * Address additional feedback (broadinstitute#7000) * Fix copy/paste error (broadinstitute#7005) * Address additional feedback * Fix copy/paste error * Trigger CI --------- Co-authored-by: Blair Murri <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * Centaur reference image test should validate symlinks [VS-796] (broadinstitute#6996) * WX-903 Pre-GHA test suite disablement * WX-877 Update CHANGELOG for release 85 (broadinstitute#7011) * Update cromwell version from 85 to 86 * WX-905 (broadinstitute#7012) Co-authored-by: Thomas Wiseman <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-719 modernize `cromwell-publish` image (broadinstitute#7013) * WX-930 Add `CODEOWNERS` file (broadinstitute#7015) * Update FiveMinuteIntro: Java 11 requirement (broadinstitute#6830) Co-authored-by: Adam Nichols <[email protected]> * WX-952 Fix Cromwell version update in Helm chart (broadinstitute#7014) * Reference Disk Manifest Builder App Test (broadinstitute#7017) * [WM-1696] Update Womtool (broadinstitute#7019) Co-authored-by: Tom Wiseman <[email protected]> * WX-958 write_map() should write its last entry with a newline (broadinstitute#7022) * Centaur slurm (broadinstitute#7083) * Remove Deploy Key (broadinstitute#7084) * WX-950 Set user agent in Java client (broadinstitute#7087) * WX-950 Upgrade Azure libs to probably fix extraneous log (broadinstitute#7088) * WX-984 Revert "WX-950 Upgrade Azure libs to probably fix extraneous log" (broadinstitute#7090) * Add cron run integrations each day of the week (broadinstitute#7089) * 85 release (#28) * Update cromwell version from 83 to 84 * BW-1255 Implement POST /runs endpoint (broadinstitute#6779) * Adding route * Fixing HTTP method error * All formFields made optional * A compliling state * Saving * Saving * All three endpoints functioning as expected; updated RESTAPI.md * Updated response for submission from 200 to 201 to pass tests * Test submission response * Moved updated submission response to askSubmit * test * updating RESTAPI.md * saving * Adding utility file for submitRequest * cleanup * Update awssdkv from 2.17.152 to 2.17.194 (broadinstitute#6814) * BW-1305 Swagger Update (broadinstitute#6818) * Properly documenting metadataArchiveStatus in WorkflowQueryResult model * Update docs * BT-710 Add configs for BlobPathBuilderFactory (broadinstitute#6817) BT-710 Add configs for BlobPathBuilderFactory * BW-1305 Make "name" optional in workflow query response (broadinstitute#6821) * BT-724 Fix BlobPathBuilder failing on retrieving existing filesystem (broadinstitute#6816) Modify blobPathBuilder to fallback to creating a filesystem if one is not found * Logging updates: (broadinstitute#6813) * [BT-698] first pass on BlobTokenGenerator with E2E test (broadinstitute#6824) * first pass on BlobTokenGenerator with E2E test * update BlobPathBuilder constructor args in test * account -> container level client * [BT-687] specify correct types (broadinstitute#6829) * specify correct types * fix test with new type * remove type declarations in function call * remove unnecessary sas-token config * BW-1206 - Combine all Wes Endpoints & add Tests (broadinstitute#6833) * Add tests, getting frid of WesRunRoutes.scala * wesWorkflowId fix, ec implicits errors gone * Refactoring path for GET /runs * Indentation fix * Commit to rollback * Revert "Indentation fix" This reverts commit 63fc484. * PR trigger * Optimize imports * Missed import * BW-1354 - Porting CBAS preliminary step (broadinstitute#6837) * Getting rid of shared utility file; Adding/Updating WES version of submit. * Edit spec file * Adding Wes-like error * BW-1378 Addl CromIAM user enablement checks (broadinstitute#6826) * Update cromwell version from 84 to 85 * BW-1393 Release doc updates (broadinstitute#6839) * BT-732 Checksum validation for blobs read by engine (broadinstitute#6838) * 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 (broadinstitute#6831) * 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 (broadinstitute#6903) * 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 * [BW-1398] Migrate PKs to BIGINT (broadinstitute#6907) * BT-745 Batch 2 of scala steward updates (broadinstitute#6906) * Update SBT to 2.0.0 * Fix sbt-git import * Update mouse to 1.0.11 * Update rhino 1.7.14 * SUP-692 Retry with more memory after RC 137 (broadinstitute#6912) * 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 (broadinstitute#6913) * Scala steward updates batch 3 * WX-745 Batch 4 scala steward updates (broadinstitute#6916) * WX-746 Localize all DRS inputs in a single Action (broadinstitute#6914) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-755 Build all images instead of just Cromwell (broadinstitute#6919) * WX-755 Add `isRelease` option for Docker builds (broadinstitute#6923) * WX-755 Cromwell/CromIAM automatically board train (broadinstitute#6924) * WX-755 Fix environment variable syntax (broadinstitute#6926) * WX-743 Enable TES task creation with BlobPaths (broadinstitute#6921) * 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 <[email protected]> * PR feedback Co-authored-by: Brian Reilly <[email protected]> * [WX-765] Update snakeyaml to 1.33 (broadinstitute#6927) * update snakeyaml to 1.33 * Don't use deprecated no-arg Constructor constructor Co-authored-by: Janet Gainer-Dewar <[email protected]> * WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (broadinstitute#6925) * Upgrade Postgres to 42.4.1 (broadinstitute#6932) * WX-735 Fix incorrect and/or nondeterministic filesystem ordering (broadinstitute#6930) * WX-772 Update Scala to 2.13.9 (broadinstitute#6928) * 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 <[email protected]> * WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (broadinstitute#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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * WX-808 Host allowlist for HTTP imports (broadinstitute#6938) * `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 <[email protected]> * Update commons text to 1.10.0 (broadinstitute#6937) * WX-751 Token refresh signal for monitoring (broadinstitute#6939) * Log messages * `DEBUG` -> `INFO` * WX-744 Optionally rewrite blob paths to appear as local paths (broadinstitute#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 <[email protected]> * Apply PR feedback in second place Co-authored-by: Adam Nichols <[email protected]> * Update changelog for wdl http allow list (broadinstitute#6944) * WM-1491 Fixing Cromwell-client (broadinstitute#6943) * More updated client for use in cbas * Removing excess code * Fix client build script (broadinstitute#6945) * WX-837: Remove CWL references from documentation (broadinstitute#6949) * 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 * WX-728 Add configurable WSM client to Cromwell (broadinstitute#6948) * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Khalid Shakir <[email protected]> * CROM-6554: Removed PAPIv1 references from doc (broadinstitute#6950) * crom-6554 removed references to PAPI v1 from doc * crom-6554 pr feedback, reworded doc to use example conf as a starting point * WX-833 Real Azure DRS Credentials (broadinstitute#6952) * Remove B2C reference from name * Get token for current user rather than getting from KeyVault * Remove KeyVault config for engine * Remove KeyVault config for DRSLocalizer * Remove KeyVault dependency * Remove KeyVault support from localizer repo template * Cleaned up and working Azure token acquisition for engine * Collapse localizer's AccessTokenStrategy into DrsCredentials * Cleanup * WX-853 Remove most CWL (broadinstitute#6955) * WX-696 Enable getting SAS token from WSM (broadinstitute#6954) * WX-696 Enable getting SAS token from WSM * Wire container resource id from config * Move resource-container-id config path * First pass at config for WSM * Remove unused singleton config * Tests for new config * Fix config parsing * Modified b2c token to be provided each time * Remove singletonConfig arg from factory * Restore types to factory configs * Clean up comments and empty token default * Default to config b2c before searching environment * Fix token default on api client * Fix test * Refactor error handling for when there is no token * Remove token constructor arg for clientProvider * Move configs to global singleton config * Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala * default -> override * Add override token to test * Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala Co-authored-by: Adam Nichols <[email protected]> * Parentheses * Reduce token timeout * Move AzureCredentials to separate file * Make AzureCredentials an object * WSM token cleanup * Config refactor (broadinstitute#6960) Co-authored-by: Janet Gainer-Dewar <[email protected]> * Initial blob token documentation * Refine language in BlobSasTokenGenerator * Update comment and formatting Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * WX-853 Remove CWL language factory, Centaur runner (broadinstitute#6961) * WX-842 Add Pact Dependency for Cromwell (broadinstitute#6962) * WX-842 Add Pact Dependency for Cromwell * Remove incomplete test spec * Initial Pact Test * Fix pact so it compiles * Add breadcrumb comment and clean up * ID-125 Add support for drshub, rename all the things (broadinstitute#6959) * Add support for drshub, rename all the things * fallback to martha if resolver is not in config * WX-867 Translate crc32c hashes to b64 for getm (broadinstitute#6970) * Translate crc32c hashes to b64 for getm * Update tests * Remove obsolete b64 handling for md5, centralize hex validation * Restore old test, fix other test * WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (broadinstitute#6965) * WX-859 Accept workflow execution identity in config (broadinstitute#6967) * WX-892 Trim down `ValueStore` logging to prevent OOMs (broadinstitute#6981) * Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (broadinstitute#6975) * WX-863 Turn off Azure NIO logging (broadinstitute#6982) * Turn off Azure NIO logging * Poke Travis * WM-1616: Allow repeating attempts at initialization (take 2) (broadinstitute#6985) * WX-878 Single shared BlobFileSystemManager (broadinstitute#6986) * Make BlobFileSystemManager shared across all BlobPathBuilders * Update TES conf file to reflect new singleton config * Shell escape reference image files [VS-796] [WX-910] (broadinstitute#6989) * WX-769 `disks` compatibility for TES backend (broadinstitute#6991) * Update FiveMinuteIntro.md (broadinstitute#6994) * WX-906 Sbt Unit Tests as Github Actions (broadinstitute#6992) * WX-926 Support falling back to OCI Manifest Format (broadinstitute#7003) * WX-926 Support falling back to OCI Manifest Forma * Only mount reference disks if requested [WX-925] (broadinstitute#7001) * [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (broadinstitute#7004) * WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (broadinstitute#6980) * WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status * Address feedback * Address feedback (broadinstitute#6997) * Address additional feedback (broadinstitute#7000) * Fix copy/paste error (broadinstitute#7005) * Address additional feedback * Fix copy/paste error * Trigger CI --------- Co-authored-by: Blair Murri <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * Centaur reference image test should validate symlinks [VS-796] (broadinstitute#6996) * WX-903 Pre-GHA test suite disablement * WX-877 Update CHANGELOG for release 85 (broadinstitute#7011) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Katrina P <[email protected]> Co-authored-by: Chris Llanwarne <[email protected]> Co-authored-by: Christian Freitas <[email protected]> Co-authored-by: Saloni Shah <[email protected]> Co-authored-by: kshakir <[email protected]> Co-authored-by: mspector <[email protected]> Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: Brian Reilly <[email protected]> Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Justin Variath Thomas <[email protected]> Co-authored-by: Christian Freitas <[email protected]> Co-authored-by: Trevyn Langsford <[email protected]> Co-authored-by: Miguel Covarrubias <[email protected]> Co-authored-by: ekiernan <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Blair Murri <[email protected]> * Remove Yaml (broadinstitute#7098) * Azure blob read/write integration test (broadinstitute#7024) Co-authored-by: Tom Wiseman <[email protected]> * Goodbye Travis (broadinstitute#7100) * Single workflow runner (broadinstitute#7106) * WX-975 Revert special TES path munging (broadinstitute#7103) * Centaur blob filesystem (broadinstitute#7104) * WX-1010 Update Github Actions set output syntax (broadinstitute#7111) * WX-1001 Upgrade JSON Small and Fast Parser (broadinstitute#7116) * WX-1015 Override glob behavior for TES to use absolute path (broadinstitute#7120) * WX-990 Make TES request backoff behavior configurable (broadinstitute#7122) * WX-1103 Revert CI to old TES polling behavior (broadinstitute#7126) * Develop aws (#29) * stuck on globbing * efs works, no callcaching * update readme * extended EFS support * fix for globbing in nested scatters * updated config for globbing, to prevent issues with empty folders * WX-1103 Accelerate TES CI (broadinstitute#7130) * Fix Horicromtal Deadlock Test (broadinstitute#7131) * WM-1963: Validate PRs begin with Jira tags (broadinstitute#7127) * WX-1106 Add logging for failed docker manifest pulls (broadinstitute#7135) Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * [WX-1108] Disable drs tests (broadinstitute#7145) * ID-377 Setup pact for consumer contract testing. (broadinstitute#7123) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1092 Support `size` engine function for public HTTP files (broadinstitute#7128) * WX-1105 Fix interpretation of full http blob paths (broadinstitute#7138) Co-authored-by: Adam Nichols <[email protected]> * Revert "ID-377 Setup pact for consumer contract testing." (broadinstitute#7146) * WX-966 Add Cascades, remove Directory from Biscayne (broadinstitute#7105) * WX-966 Post-merge branch cleanup + test fix (broadinstitute#7149) * WX-1122 Enable Azure ApplicationInsights (broadinstitute#7143) * [WX-1108] Add tests back (broadinstitute#7148) * [WX-1136] Docker Build Test (broadinstitute#7151) * [WX-1136] Self Hosted (broadinstitute#7152) * WX-1145 Fix minor regression introduced in WDL 1.1 foundation (broadinstitute#7153) * ID-377 Setup pact for consumer contract testing. Retry (broadinstitute#7147) Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Ivan <[email protected]> * WX-1133 Shorten TES localized blob paths (broadinstitute#7150) * WX-1154 Fix Slack Messaging (broadinstitute#7159) * efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs (#32) * WX-1160 Fix bad MariaDB version assumptions (broadinstitute#7160) * WX-1126 Upgrade to modern Python, 3.8 not available in package repo anymore (broadinstitute#7164) * WX-1122 Use legacy AppInsights to get better control over logging (broadinstitute#7157) * WX-1137 Replace 4-byte unicode chars in PAPI event descriptions (broadinstitute#7166) * WX-1101 Update library versions to support batch (broadinstitute#7155) Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1195 Update Azure identity libs (broadinstitute#7173) * WX-1114 Initial inclusion of Azure NIO 'fork' (broadinstitute#7168) * WX-1110[risk=low] Added endpoint to fetch failed tasks by root workflow id (broadinstitute#7165) * WX-1210 Added JIRA ID for Cromwhelm auto commit message (broadinstitute#7180) * WX-1179 DRS image build updates, remove self-hosted runners (broadinstitute#7179) * WX-1210-action-fix Use PR title to find JIRA ID for cromwhelm commit message (broadinstitute#7184) * WX-1110-query-fix Corrected Query to pull in attributes outside of executionStatus and backendStatus (broadinstitute#7185) * WX-1179 GCP Batch new base (broadinstitute#7177) Co-authored-by: dspeck <[email protected]> Co-authored-by: jarroyo28 <[email protected]> Co-authored-by: Jacob Jennings <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Chris Llanwarne <[email protected]> Co-authored-by: Christian Freitas <[email protected]> Co-authored-by: Tristan Garwood <[email protected]> * WM-2100: Update terra-helmfile on publish (broadinstitute#7187) * WM-2100: Correct commit and PR description of terra-helmfile auto update (broadinstitute#7188) * WX-1230 Ignore `invalidate_bad_caches_use_good_local.test` (broadinstitute#7197) * WX-1078 ACR support (broadinstitute#7192) * WX-1179 Enable GCP Batch Integration Tests (broadinstitute#7199) Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * WX-1179 GCP Batch Docs Update (broadinstitute#7196) Co-authored-by: Jacob Jennings <[email protected]> Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * ID-734 Increase Timeout for DRSHub Communication (broadinstitute#7198) * [WX-1156] internal_path_prefix for TES 4.4 (broadinstitute#7190) * [WM-2184] Remove brackets from Jira ID (broadinstitute#7206) * WX-1153 Azure blob read md5 from metadata for large files (broadinstitute#7204) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1156 Fix internal_path_prefix (broadinstitute#7208) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1256 Temporarily turn off engine hashing for blob files (broadinstitute#7209) Co-authored-by: Adam Nichols <[email protected]> * WX-1173 Reopen filesystem for blob storage outside workspace (broadinstitute#7178) Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Adam Nichols <[email protected]> * WX-1174 Adjust NIO Copy functionality (broadinstitute#7207) Co-authored-by: Adam Nichols <[email protected]> * [WX-1168] TES Log Paths (broadinstitute#7210) * Develop aws (#34) * efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs * add deployment manual, fix issue with empty disks * update documentation * update documentation * update documentation * WX-1264 Don't expire an unexpirable filesystem (broadinstitute#7216) * [WX-495] DRS Parallel Downloads (broadinstitute#7214) * WX-1225 Print TES error messages to job logger (broadinstitute#7220) * WX-1217 Workflow completion callback (broadinstitute#7213) Co-authored-by: Chris Llanwarne <[email protected]> * [WM-2199] Changeset for modifying ownership of tables for WORKFLOWS app (broadinstitute#7218) Co-authored-by: Chris Llanwarne <[email protected]> * [WX-1234] Update CHANGELOG.md (broadinstitute#7227) Merging past CI since this is doc only. * WM-2252: Configurable metadata write role (broadinstitute#7225) Co-authored-by: dvoet <[email protected]> * Update cromwell version from 86 to 87 * WX-1282 Update failedJobs Query to use `lo_get` instead of INNER JOIN against pg_largeobject (broadinstitute#7228) * [WX-1234] Update Release Process with Docker Instructions (broadinstitute#7231) Co-authored-by: Adam Nichols <[email protected]> * WM-2294: Allow role-setter action to run on change (broadinstitute#7233) * WM-2296: Callback should supply fully qualified output names (broadinstitute#7234) * [WX-499] DRS Parallel Downloads Follow-up (broadinstitute#7229) * WX-1318 gcp batch: Add GPU driver install (broadinstitute#7235) Co-authored-by: Adam Nichols <[email protected]> * WX-1232 Include useful workflow ids in TES tags (broadinstitute#7221) * Options to publish status only (#36) * add options to publish status only * updated readme.md --------- Co-authored-by: quekx <[email protected]> * WX-1307 Azure E2E test (broadinstitute#7239) Co-authored-by: Janet Gainer-Dewar <[email protected]> * Fix aws unit tests (#39) * checkpoint * fix ecr and batch tests * fix AwsBatchJobSpec.scala --------- Co-authored-by: quekx <[email protected]> * return bucket directly instead of listing and checking it (#38) Co-authored-by: quekx <[email protected]> * WX-1340 GCP Batch: Mount with extra colon issue and multiple zones support (broadinstitute#7240) Co-authored-by: Adam Nichols <[email protected]> * WX-1339 Make `throwExceptionOnExecuteError` false for PAPI aborts (broadinstitute#7245) * WX-1338 Fix cron invocation of E2E test (broadinstitute#7244) * WX-1341 Better logging when a runner stops picking up new workflows (broadinstitute#7246) * Add evaluteOnExit for aws batch retry (#40) Co-authored-by: quekx <[email protected]> * [WX-1260] Acquire sas token from task runner (broadinstitute#7241) Co-authored-by: Adam Nichols <[email protected]> * [WX-1183] Ice Lake (broadinstitute#7252) * WX-1333 Improve logging visibility for load management (broadinstitute#7253) * [WX-1391] Fix Bash Bug (broadinstitute#7326) * [WX-1393] Add Content Length to Curl request (broadinstitute#7328) * [WX-1346] Scalafmt (broadinstitute#7257) * WX-1351 Speed up `Centaur Horicromtal PapiV2 Beta` (broadinstitute#7329) * WX-1351 CI CWL cleanup (broadinstitute#7327) * WX-1351 Remove slow/misbehaving localization test (broadinstitute#7330) * WX-1351 Split out restart tests (broadinstitute#7333) * [WX-1345] Automatic Token Acquisition for TES Config (broadinstitute#7256) * WX-1387 Remove unused case classes (broadinstitute#7334) * [WX-1394] Upgrade Logback Core to address CVE-2023-6378 (broadinstitute#7332) * WX-1351 Another round of CI cleanup (broadinstitute#7336) * [WX-1395] Scalafmt GitHub Action (broadinstitute#7337) * WX-1351 SBT compile speedup (broadinstitute#7339) * WX-1407 Fix contract tests (broadinstitute#7340) Co-authored-by: Ivan <[email protected]> * WX-1409 Java 17 (broadinstitute#7342) * Revert "WX-1409 Java 17 (broadinstitute#7342)" (broadinstitute#7343) * WX-1409 Restore Java 17 (broadinstitute#7342) (broadinstitute#7344) * Revert "WX-1409 Java 17" (broadinstitute#7346) * [WX-1395] Scala formatter Github Action (broadinstitute#7341) Co-authored-by: ScalaFmt Fixer <[email protected]> Co-authored-by: Broad Bot <[email protected]> * Improved tagging support (#37) * efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs * add deployment manual, fix issue with empty disks * update documentation * update documentation * update documentation * support for tagging instances and volumes used in jobs, some support for spaces in file paths * corrected workflow id in tagging * redirect exit code 137 to retry-with-more-memory routine --------- Co-authored-by: Henrique Ribeiro <[email protected]> * add gpu count (#41) * add gpu count * fix typo --------- Co-authored-by: quekx <[email protected]> Co-authored-by: Henrique Ribeiro <[email protected]> * WX-1385 Reject blob URLs with external SAS tokens as unparsable (broadinstitute#7347) * WX-1411 Require preinstalled `jq` and `curl` for just-in-time SAS feature (broadinstitute#7350) * WX-1396 Cromwell client allow additional properties (broadinstitute#7352) * WM-2428: Include full error context when failing to abort TES jobs (broadinstitute#7354) * WX-1420 Fix GCP Batch label regex restriction (broadinstitute#7355) Co-authored-by: Beibei Chen <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1385 Remove SAS tokens from TES input log printouts (broadinstitute#7358) * [WX-1184] PostgreSQL Docker Image for Local Cromwell (broadinstitute#7172) Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1444 Use MySQL LTS in DBMS tests (broadinstitute#7360) * WX-1449 Add `latest` Docker tag (broadinstitute#7362) * WX-767 Upgrade Cloud SDK to 461.0.0 (broadinstitute#7361) * WX-1443 Adopt `gcloud storage` for localization only (broadinstitute#7359) * WX-964 suffix() (broadinstitute#7363) * WX-1417 New database role strategy (broadinstitute#7366) * [WM-2291] Callback API contract tests between Cromwell and CBAS (broadinstitute#7251) Co-authored-by: Chris Llanwarne <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * WX-1445 Update docker image regex to handle python:3 correctly (broadinstitute#7367) * WX-1252 Runtime attributes cleanup – CWL runtime attributes (broadinstitute#7370) * WX-1485 Upgrade postgres lib (broadinstitute#7371) * WM-2454: Private GitHub support on describe api (broadinstitute#7365) * WX-1252 Runtime attributes cleanup – CWL runtime environment (broadinstitute#7369) * WX-1462 POSIX-flavored sub() (broadinstitute#7374) * [WX-963] Unzip Engine Function (broadinstitute#7368) * WX-1489 Hopefully reduce CI flakiness by modernizing deadlock test (broadinstitute#7376) * [WX-965] quote() and squote() engine functions. (broadinstitute#7375) Co-authored-by: Ryan Saperstein <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> * [WX-1317] Remove Akka 'server' header from all HTTP responses (broadinstitute#7379) * WM-2461] Add support for running private workflows on Azure (broadinstitute#7373) * WX-1252 Per-backend runtime attributes (broadinstitute#7380) * ID-347 Remove Martha References (broadinstitute#7384) * WX-1461 Remove `womtool upgrade` command (broadinstitute#7382) * WX-1488 Supply cloud platform when making DRS requests (broadinstitute#7381) * WX-757 Fix workflow stuck in aborting after WDL type error (broadinstitute#7385) * [WX-1506] Add jobLogger output for subworkflow running (with parent and subworkflow ID) (broadinstitute#7388) Co-authored-by: jlester-msft <[email protected]> * WX-757 Fix `stdout`, `stderr` in workflow body causing crashes (broadinstitute#7386) * WX-1519 Stop leaking DRS Localizer images on every CI run (broadinstitute#7390) * [WX-1460] WDL 1.1 Struct Literal Parsing (broadinstitute#7391) Co-authored-by: Janet Gainer-Dewar <[email protected]> * [WM-2500][WM-2502] Fetch Github token from ECM for importing and running private workflows (broadinstitute#7392) * WX-1542 Fix workflow cancellation (broadinstitute#7398) * WX-1550 Don't pointlessly continue running integration tests (broadinstitute#7400) * WX-1557 Fix default values from Configuring.md and Scaling.md (broadinstitute#7393) Co-authored-by: Adam Nichols <[email protected]> * WX-1557 Fix actor-factory in Batch101.md (broadinstitute#7377) Co-authored-by: Adam Nichols <[email protected]> * WX-1557 Add more tests to the GCP Batch backend (broadinstitute#7394) Co-authored-by: Adam Nichols <[email protected]> * [WX-1531] Struct Literal Type Checking (broadinstitute#7402) * [WX-1468] Implement `returnCodes` runtime attribute (broadinstitute#7389) Co-authored-by: Ryan Saperstein <[email protected]> Co-authored-by: Ryan Saperstein <[email protected]> * [WM-2555] Cromwell -> ECM contract test (broadinstitute#7405) * [WX-1568] Bump Akka max-response-reason-length limit (broadinstitute#7406) * WX-1530 Strip pesky URL bits when creating local paths for HTTP inputs (broadinstitute#7404) * WX-1538 Add more tests to the GCP Batch backend (broadinstitute#7410) * [WX-1605] Fix Codecov Report Uploads (broadinstitute#7418) * [WX-1410] Sanitize 4 byte UTF-8 characters before inserting into METADATA_ENTRY (broadinstitute#7414) * WX-1566 Special Docker build for debugging (broadinstitute#7417) Run `sbt -Dproject.isDebug=true server/docker` * [WX-1448] Add verbose logging and timeout for getm (broadinstitute#7416) Co-authored-by: Adam Nichols <[email protected]> * WX-1566 Fix Morgan's call cache file hash CPU thrash Cromwell crash (broadinstitute#7419) * WX-1566 Fix RTD so this ticket's docs get published (broadinstitute#7420) * fix womFileType coercion (#47) Co-authored-by: quekx <[email protected]> * PR #44: Multi-aserisk globbing by @kevinRenaersBio. Reapplied selection of changes on aws_develop branch * PR #45 reapplied to aws_develop: support for sharedMemory. skipped EFS fixes for now while waiting for feedback * upstream PR broadinstitute#7488 : fix compilation error due to swagger2markup * Fix issue with caching on EFS by replacing touch with existOrThrow routine * make sure that md5 sibling file of EFS data is newer than main file to be valid * revise sharedmemory attribute to take reguluar GB/MB specification * updated AWS README file --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Janet Gainer-Dewar <[email protected]> Co-authored-by: Christian Freitas <[email protected]> Co-authored-by: Saloni Shah <[email protected]> Co-authored-by: Brian Reilly <[email protected]> Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: Katrina P <[email protected]> Co-authored-by: Adam Nichols <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chris Llanwarne <[email protected]> Co-authored-by: Justin Variath Thomas <[email protected]> Co-authored-by: Khalid Shakir <[email protected]> Co-authored-by: Christian Freitas <[email protected]> Co-authored-by: Trevyn Langsford <[email protected]> Co-authored-by: Miguel Covarrubias <[email protected]> Co-authored-by: ekiernan <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Blair Murri <[email protected]> Co-authored-by: Thomas Wiseman <[email protected]> Co-authored-by: Tom Wiseman <[email protected]> Co-authored-by: Stephen Fleming <[email protected]> Co-authored-by: Henrique Ribeiro <[email protected]> Co-authored-by: mspector <[email protected]> Co-authored-by: Tristan Garwood <[email protected]> Co-authored-by: Ivan <[email protected]> Co-authored-by: dspeck1 <[email protected]> Co-authored-by: jarroyo28 <[email protected]> Co-authored-by: Jacob Jennings <[email protected]> Co-authored-by: Dillon Scott <[email protected]> Co-authored-by: Chris Llanwarne <[email protected]> Co-authored-by: dvoet <[email protected]> Co-authored-by: xquek <[email protected]> Co-authored-by: quekx <[email protected]> Co-authored-by: ScalaFmt Fixer <[email protected]> Co-authored-by: Broad Bot <[email protected]> Co-authored-by: Beibei Chen <[email protected]> Co-authored-by: Maria Yazykova <[email protected]> Co-authored-by: rsaperst <[email protected]> Co-authored-by: Ryan Saperstein <[email protected]> Co-authored-by: jlester-msft <[email protected]> Co-authored-by: Alexis Hernandez <[email protected]> Co-authored-by: dkj <[email protected]> Co-authored-by: Ryan Saperstein <[email protected]> Co-authored-by: Alexis Hernandez <[email protected]>
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See https://broadworkbench.atlassian.net/browse/WM-2296