bug: remove duplicate user_router test #1736
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Reviewer's guide (collapsed on small PRs)Reviewer's GuideThe pull request cleans up the CMake test configuration by removing a redundant registration of the user_router unit test in core/database/CMakeLists.txt. File-Level Changes
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JoshuaSBrown
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Type: Bug
JoshuaSBrown
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1735-DAPS-bug-user-router-test-CMakeLists.txt-duplication
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nedvedba
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Nov 17, 2025
* [DAPS-1630] - Bug core metrics update (#1632) * refactor: remove system secret from http params. * fix: metricsUpdateMsgCounts and newJsonMetricParse methods. * feat: add test_DatabaseAPI test to core server CMakeLists.txt * [DAPS-1609] Move dependency build to submodule (#1624) * refactor: move base image check to separate stage and file. * refactor: add .gitlab-ci.yml and stage_image_check.yml files. * refactor: create custom script for base image check job. * refactor: add compressed file extensions to gitignore. * fix: correct url from pipeline to trigger/pipeline * fix: update docker dependencies file to latest commit which includes package.json. * refactor: rely on dependencies from downstream pipeline. * refactor: add common library that was missing from repo, foxx and core. * refactor: fix build-arg for intermediate build. * refactor: switch gcs image to using correct dependencies image. * fix: remove compose build of old Dockefile.dependencies. * fix: add ability to make changes in config folder. * refactor: remove common from foxx docker container build, it should not be needed. * fix: add missing LD_LIBRARY_PATH before curl command in install_foxx.sh script. --------- Co-authored-by: nedvedba <[email protected]> * [DAPS-1625] - user id map for session key josh (#1644) (#1647) * [DAPS-1625] fix bug in session and transient keys. --------- Co-authored-by: AronPerez <[email protected]> * Update devel from staging (#1649) * Update issue templates * Update issue templates * Update pull_request_template.md (#1433) * [Release] v3.13.01 Resolve Master Branch Diff (#1485) * Address formatting of jquery file * add more descriptive posix path error message * Remove redundant password file creation command * Add eslint plugin for jsdoc to github action * Update esling.config.js to error if invalid jsdoc * Add missing eslint jsdoc plugin * Remove non existant rule * Fix jsdoc issues in data_router * Fix JSDOc issues in process.js fiel * Fix JSDOc issues in repo_router.js * Address JSDoc in tasks.js * Address JSDoc linting issues * Switch to ignores statement * Address more eslint jsdoc items * Be more selective about eslint rules * Remove requrie description because seems to be faulty * Address finicky jsdoc linter * Fix js formatting * Feature DLT 1109 foxx new token data (#1194) * Stub logic for updating related edge in router function for token/set * Include logic for conditionally updating token data and pushing data to edge. * Change token_key to remove illegal characters * Fix object attribute call * Formally add query params to function. Extract query params near start of action. Check both exist before taking action on edge. Update comments, notes, TODOs * Stub testing for user_router * Fix naming of user_router test so it will be picked up with sane specification. Add test to CMakeLists * Add some fixtures for creating related user to allow for integration testing * Fix manifest json. Hard code user collection check. Set time variable. * Use correct path for router to user endpoints. Extract some query params for validation. * Remove intentionally failing test. Break now working test into logical sections. Update comments. * Add test for new features * Add further validation of no unexpected side-effects * Remove extraneous user document checks and comments * More testing for branches in introduced logic. Additional check on newly inserted globus_coll * assert -> expect * Work around multiple access and ordering issue by utilizing more test user fixtures. * Rearrange key for token edge, add suggested fields to documents * Pull user_doc from existing logic. Use object destructuring. Add error condition. Introduce protobuf enum to backend. Add parser for other_token_data string. Update document creation functions * Extract fixture build call to separate script. Add script as fixture in cmake * Remove some extraneous logic, remove password file overwrite. * Remove unused zeromq flag * Adjust testing to include enum, expect error on invalid input combination, typo, naming * Adjust scope string in user_router test. Add validations to parseOtherTokenData. Add tests for positive and error cases of parseOtherTokenData. * Change chai expects in support.test.js to use callable. Update perms on fixture setup script. Use URL encoded pipe character in user_router.test.js * Group OR in user_router.js * Adjust user_router.test.js integration tests to access deconstructed other_token_data * Add baseline jsdoc for parse method. Remove some unwanted data from globus_token doc insert * Add GLOBUS_DEFAULT to AccessTokenType enum. Add default to user_router endpoint param. Update logic to switch based on enum. Test new change by specifying default type and other_token_data. Fix name of test. * Move query parameter validations earlier in function. Decrease nesting of switch logic. * Cleanup some whitespace changes, add desired comments on assumptions. * Formatting * Fix naming for support test so they will run. * Update CHANGELOG.md with changes in minor feature. Update comments on user_router.js for saving a new globus_coll * Add comment about more fields in support.js::parseOtherTokenData * Fix issue for formatter * Add expiration check * Commit for CI * Formatting --------- Co-authored-by: Anthony Ramirez <[email protected]> * Add ci jobs to improve security posture * Change to unit stage for testing * Remove sast job * Attempt to fix semgrep sast job failure * Debug jobs * Add test stage for sast template job * Add missing test stage * Add dependency scanning * Split sast into separate test stage * Remove commented out line * Remove extra comment that is unused * Debugging log failure * Address jsdoc and typo in description * Remove outdated comments * Make comments JSDoc compliant * Address formatting inconsistency * Account for multiple images returned in log * Update .gitlab/common.yml Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Debugging log container matching * Fix typo in gitlab anchor * Debug escape anchor * Debug * Debug anchor 2 * Debug anchor 3 * Debug anchor 4 * Debug anchor 5 * Debug 6 * Debug 7 * Debug 8 * Fix names of containers from gcs-authz to gcs * Cleanup add comment back in * Update common.yml * Remove Exports * Update data_router.js Remove nested docs. * Update repo_router.js * Update task_router.js * Update eslint.config.js * Update eslint.config.js * fix jsdoc comment in posix path * Address JSDOc complaints * Address JSDoc errors * Address linter * Address linter errors * Fix order of parameters * Apply formatting * Add missing argument form strategy method call * Apply prettier * Update posix_path.js * Address ai suggestion about better error message * Debugging log failure * Account for multiple images returned in log * Update .gitlab/common.yml Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Debugging log container matching * Fix typo in gitlab anchor * Debug escape anchor * Debug * Debug anchor 2 * Debug anchor 3 * Debug anchor 4 * Debug anchor 5 * Debug 6 * Debug 7 * Debug 8 * Fix names of containers from gcs-authz to gcs * Cleanup add comment back in * Update common.yml * Remove Exports * Cleanup comments and apply formatting * Update nlhoman json version * Update protobuf versions * Add tests for authz router * Specify ubuntu 20.04 explicitly * Revert dependency versions * Fix problems with path consistent method * Cleanup javascript * Format javascript * Feature DLT 1127 relay new token data (#1217) * Add additional params to DatabaseAPI::userSetAccessToken to pass message with addtional info on to database API. * Add convenience method with old type signature of DatabaseAPI::userSetAccessToken for compatibility * Conditionally add other token options param when calling dbGetRaw. * Pass token type along to Database API. * Pass token type from message. * Extract logic for building URL from dbPost and dbGetRaw into separate function for easier testing and debugging * Extract url building logic from dbGet * Add some comments for moved code, address a TODO, add new TODO for AccessToken Message type field * Address default on token type, formatting * Add new AccessTokenType entries for a sentinel value and Globus default in SDMS.proto, use as desired in DatabaseAPI.cpp * Change query param to match backend changes * Restore formatting of SDMS.proto * Make built URL const where appropriate in DatabaseAPI.cpp and DatabaseAPI.hpp * Change default AccessTokenType for UserSetAccessTokenRequest in SDMS_Auth.proto. * Remove logging of potentially senitive data * Adjust AccessTokenType ACCESS_SENTINEL to have value of uint8 max. --------- Co-authored-by: Anthony Ramirez <[email protected]> * [DLT-1110] Update files with prettier [DLT-1110] Add controller unit tests [DLT-1110] Remove debug [DLT-1110] Correct import statements, endpoint list [DLT-1110] Refactor out into MVC [DLT-1110] Add debug [DLT-1110] Functioning modal, needs refactoring [DLT-1110] Refactor dlg start transfer using OOO programming. Should be MVC cased on what I'm seeing but we'll see * [DLT-1110] Split branches * [DLT-1110] Update model, make logic private, remove controller form transfer request when update or get * [DLT-1110] Add commnets to logic * [DLT-1110] Correct HTML escape, francy tree init * [DLT-1110] Pull out template HTML * [DLT-1110] Fix update bug * [DLT-1110] Dependency injection * [DLT-1110] Update if statements * [DLT-1110] Update style * Revert "[DLT-1110] Mapped Collection Endpoint Browse (1/4)" * Address eslint * Address remaining eslint items * Fix bug on task_router.js abort function (#1234) Co-authored-by: Anthony Ramirez <[email protected]> * Address Aaron feedback * applied potential fix to deprecation warning * Reorder createRecord * Apply formatting * Throw error if OpenStack error code returned from API * Add dependency between logs * Add dependencies on end to end jobs as well * Job rule is not supported * Remove always run log * add end to end signal job * Fix tag of signal * Feature DLT 1120 retrieve transfer token (#1228) * Add conditional switch and stub some logic for handling other resources in callbacks * Fix order of logging. Add redirect * Debug logging for web service. Attempt to set token. * Remove incorrect method call to data, use data attribute. * Add some TODOs and logging * Give setAccessToken ability to accept additional params to pass to protobuf * Add additional params to DatabaseAPI::userSetAccessToken to pass message with addtional info on to database API. * Add convenience method with old type signature of DatabaseAPI::userSetAccessToken for compatibility * Conditionally add other token options param when calling dbGetRaw. * Pass token type along to Database API. * Pass token type from message. * Stub logic for updating related edge in router function for token/set * Include logic for conditionally updating token data and pushing data to edge. * Change token_key to remove illegal characters * Fix object attribute call * Prettier formatting for datafed-ws.js * Roll back changes to DatabaseAPI.hpp and DatabaseAPI.cpp that are covered in #1127 * Refactor new inclusions in datafed-ws.js to use as much existing code as possible, only diverge where necessary. * datafed-ws.js change scopes to scope * datafed-ws.js log user ID array * datafed-ws.js clarify uid assignment at ui/authn endpoint, add note on error cases, remove incorrect comment about uid, add appropriate error if collection_id not present * datafed-ws.js Extract AccessTokenType enum, add comment about fetching from protobuf; remove unnecessary commented code * datafed-ws.js Extract transfer set logic when calling setAccessToken to improve readability of router. * datafed-ws.js Create function for resolving token type; create function to handle logic in building optional_data for setAccessToken; reduce unneccessary nesting in ui/authn endpoint * datafed-ws.js Fix spacing, fix typo in variable name * datafed-ws.js Fix bug referring to request session * datafed-ws.js Nesting was necessary. * datafed-ws.js Address some TODOs, set token type with more context * datafed-ws.js Remove some additional extraneous logging * datafed-ws.js Formatting * Add comment about token set * datafed-ws.js Update deprecated substring method, Fix order for error case when new user receives transfer token * TokenHandler.js Refactor token handling logic out of web server main. datafed-ws.js User new OAuthTokenHandler class to handle token logic. * TokenHandler.js Implement token validator; move OAuthTransferToken def to top. TokenHandler.test.js Minimal testing of token handler * TokenHandler.test.js Add tests for case when resource server is auth * TokenHandler.test.js Add testing for Globus transfer resource server * TokenHandler.js Implement validation for existence of required keys. TokenHandler.test.js Adjust other_tokens fixtures to be nested according to incoming data; formatting. * datafed-ws.js formatting * TokenHandler.js Update error messages, remove unnecessary code in getTokenType, returns in resolveTokenType * datafed-ws.js Add error handling around token_handler construction; add errors and handling for setAccessToken, JSDoc. * datafed-ws.js Remove hard coded collection_id. * datafed-ws.js Remove thrown errors in nested functions; single redirect. --------- Co-authored-by: Anthony Ramirez <[email protected]> * Bug daps 1243 datafed web logging (#1251) * datafed-ws.js Reverse order of LogLevel object properties * datafed-ws.js Throw error so stack trace is adequately populated * Revert line number * TokenHandler.js Fix linting errors. --------- Co-authored-by: Anthony Ramirez <[email protected]> * [DLT-1110] Mapped Collection Endpoint Browse (1/4) (#1240) * [DLT-1110] Update style [DLT-1110] Update if statements [DLT-1110] Dependency injection [DLT-1110] Fix update bug [DLT-1110] Pull out template HTML [DLT-1110] Correct HTML escape, francy tree init [DLT-1110] Add commnets to logic [DLT-1110] Update model, make logic private, remove controller form transfer request when update or get [DLT-1110] Split branches [DLT-1110] Update files with prettier [DLT-1110] Add controller unit tests [DLT-1110] Remove debug [DLT-1110] Correct import statements, endpoint list [DLT-1110] Refactor out into MVC [DLT-1110] Add debug [DLT-1110] Functioning modal, needs refactoring [DLT-1110] Refactor dlg start transfer using OOO programming. Should be MVC cased on what I'm seeing but we'll see * [DLT-1110] Mapped Collection Endpoint Browse Tests (2/4) (#1207) * [DLT-1110] Add tests * [DLT-1110] Update chai with mocha, attempt usage of mock-import * [DLT-1110] Add mocha config, correct prettier * [DLT-1110] Update tests, correct logic * [DLT-1110] Update tests, add fixtures, update setup, lock in packages * [DLT-1110] Update test * [DLT-1110] Config * [DLT-1110] Upgrade node v14 -> v23 * [DLT-1110] Upgrade node v23 -> v18, better jump * [DLT-1110] Correct ver .sh file * Revert "[DLT-1110] Correct ver .sh file" This reverts commit 5c78c59. * Revert "[DLT-1110] Upgrade node v23 -> v18, better jump" This reverts commit 9d66847. * Revert "[DLT-1110] Upgrade node v14 -> v23" This reverts commit fb8b93d. * Revert "[DLT-1110] Config" This reverts commit 82715f0. * Revert "[DLT-1110] Mapped Collection Endpoint Browse Tests (2/4) (#1207)" This reverts commit 22545fa. * added updated version t0 requirements.txt * Fix edge case in GridFTP Authz where '/' is used * cpp-py-formatter * Add changelog comment * Address prettier formatting * Add method for testing config, fix bug in global config, fix redundant log statements * Make error detection clearer in bool * Add mock core server * Add integration and, liveness test for mock * Address mock integration setup and consolidate * Apply formatting * Remove unused timeout variable from mock * Address JSDoc complaints * Apply prettier * Fix formatting and eslint prettier issues * Address codacy feedback * Add changelog comment * Clean up grammar in comment * Add note in Config.h * Apply clang formatting * Address codacy issues * Add env var * Update Arangodb packaged version to using 3.12.4 * Fix confusion in key uses in end to end tests * Add change log comment * Add changelog comment * corrected imported member * Add compose entries for foxx tests * Update the schema documentation to improve the usability. * Add example schema with a reference * Add notebook for linting jupyter * Using working directory option * Update .github/workflows/jupyternotebook-lint.yml Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Update python notebooks * Attempt to fix jupyternote book linting errors * Format with black * Specify line length with black to be consistent with flake8 * Add a Changelog comment * Change line length to 88 * Add black formatters * Make formatting consistent across project * Fix linter * Temporarily keep line length in black to 79 and address in separate issue * Change line length to 88 for now : * updated changelog * Fix bug in CI scripts associated with repo and gcs image build * Merge hotfixes into devel (#1326) * [DAPS-DEPS] Update cpp-py-formatter to 0.3.0 * [DAPS-DEPS] Update cpp-py-formatter to 0.3.1 * [DAPS-DEPS] Update ver, add push * updated versions for release * Update project.rst * Update format-check.yml * Pull in version numbers appropriately * Avoid build cache * Aggressive prune * Trigger rebuild * generate_repo_config.sh Accept env variable for datafed server from repo service instead of hard coding * Allow core config thread options to be read in from env * Add changelog comment * Adjust deployment version number * Fix Version month * Update CHANGELOG.md Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> --------- Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: JoshuaSBrown <[email protected]> Co-authored-by: Anthony Ramirez <[email protected]> Co-authored-by: nedvedba <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Feature DAPS 1215 foxx UserGetAccessTokenRequest mapped collection support (#1284) * Begin prototyping required code for mapped collection token retrieval. * SDMS_Auth.proto Add optional fields to UserGetAccessTokenRequest and UserAccessTokenReply to support finding correct tokens * user_router.js Add baseline query params and checks. DatabaseAPI.cpp & DatabaseAPI.hpp Use updated names and types. ClientWorker.cpp Update comments. * user_router.js Add logic for finding token based on collection; add token match and missing match cases * Return necessary data from Database to refresh tokens. Mock data on dir/list to test out changes. * user_router.js Add check for existence of Globus collection * user_router.js Remove existence check, move to filter method; Add notes on covered cases; add notes on code * datafed-ws.js Temporary handling of need consent response. * user_router.js Add queryParam validation for new params via joilib. ClientWorker.cpp Add refresh token try/catch to send through flow if refresh fails * datafed-ws.js Use correct converted casing for protobuf messages; redirect to error when needs_consent * datafed-ws.js No redirect, show error directly in list. * datafed-ws.js Early return to prevent further requests * support.js Update AccessTokenType enum. user_token.js New class introduced for handling logic for validating params when getting tokens and building GetAccessToken responses. user_router.js Replace logic with calls to new lib * user_token.js Add jsdoc definition for return type and format function. user_router.js Remove unnecessary comment. * user_token.js More jsdoc definition; Add validation for collection token document required fields. user_token.test.js Add preliminary unit tests for static methods. * CMakeLists.txt Add new unit tests to build. user_token.test.js Modify naming to match convention. * CMakeLists.txt Fix variable get. user_token.js Fix export. * user_fixture.js Add new user for get/token tests. user_router.test.js Add simple tests for get/token endpoint. user_token.js Fix naming for token document scopes field. user_token.test.js Changes for scope field bugfix. * user_router.js Formatting; Throw error if more than one token matches, add note about token type. * ClientWorker.cpp Address some TODOs and extraneous comments. DatabaseAPI.cpp Remove TODOs. SDMS_Auth.proto Remove unused field. * user_token.js Update formatUserToken to always return object values. DatabaseAPI.cpp Add note on possibly missing field. user_token.test.js Update tests to check for new expected values. * user_router.js Clean up some comments for clarity. datafed-ws.js Formatting. * ClientWorker.cpp Rewrite comment regarding mapped token refresh. * user_token.js Formatting. * CHANGELOG.md update for feature * user_router.js Re-introduce accidentally removed `globus_collection` object. * CMakeLists.txt Remove comment about necessity * Update token lookup logic to use `byExample`, add test case for missing Globus collection. Add globus_coll fixture. * SDMS_Auth.proto Change UserAccessTokenReply needs_consent to optional field. * user_router.js Update token/get to default to start consent flow when collection tokens are present. user_router.test.js Update test from error to needs_consent. * Formatting changes. --------- Co-authored-by: Anthony Ramirez <[email protected]> * [DLT-1110] Implement Consent Required Action (3/4 & 4/4) (#1242) * [DLT-1110] Refactor browse into component and use CSS * [DAPS-1110] Update * [DAPS-1110] Update web server * [DAPS-1110] add refactors * [DAPS-1110] Prettier * [DAPS-1110] Refactor tests * [DAPS-1110] Remove .. in ep ls, remove logs * [DAPS-1110] Add sinon, remove dead code * [DAPS-1110] Address transfer start button bug * [DAPS-1110] eslint, update api.test.js to reflect usage * [DAPS-1110] format * [DAPS-1110] Correct bug * JSON parse error fix (#1328) * DatabaseAPI.cpp Pull in json dependency, use json object to serialize request payload * Replace json serialization in more locations where parseSearchRequest is being called. * Add comments around locations that will need json serialization * Convert missed body append to serialization format * typo * Refactoring DatabaseAPI.cpp to incorporate json serialization * More serialization work * Pull in changes from 1214 for dataPut * Bring in changes from 1214 for dataGet * DatabaseAPI.cpp Fix error with missing curly brace. Some formatting that is likely wrong. Serialize up to original point. Need to validate. * Add missing scope resolution * More typos * More typos. Scoping * Remove non-existant vars * declare body * Formatting * Formatting and verification of updates * Replace most places * Formatting * Remove redeclaration * DatabaseAPI.cpp Remove some comments. * DatabaseAPI.cpp Add missing push_back * Adding braces * Prevent Double Escaping string, by using nlohmann json parse to read in value. * remove escapeJSON calls, redundant with nlohmann json dump * Allow parsing for metric data to be run in parallel for now, output messages when old serialization is used. * Ensure ASCII setting. * Upgrade debug to warning. --------- Co-authored-by: Anthony Ramirez <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Joshua S Brown <[email protected]> * Feature - Mapped Collection Token Support (#1334) * Begin prototyping required code for mapped collection token retrieval. * SDMS_Auth.proto Add optional fields to UserGetAccessTokenRequest and UserAccessTokenReply to support finding correct tokens * user_router.js Add baseline query params and checks. DatabaseAPI.cpp & DatabaseAPI.hpp Use updated names and types. ClientWorker.cpp Update comments. * user_router.js Add logic for finding token based on collection; add token match and missing match cases * Return necessary data from Database to refresh tokens. Mock data on dir/list to test out changes. * user_router.js Add check for existence of Globus collection * user_router.js Remove existence check, move to filter method; Add notes on covered cases; add notes on code * datafed-ws.js Temporary handling of need consent response. * user_router.js Add queryParam validation for new params via joilib. ClientWorker.cpp Add refresh token try/catch to send through flow if refresh fails * datafed-ws.js Use correct converted casing for protobuf messages; redirect to error when needs_consent * datafed-ws.js No redirect, show error directly in list. * datafed-ws.js Early return to prevent further requests * support.js Update AccessTokenType enum. user_token.js New class introduced for handling logic for validating params when getting tokens and building GetAccessToken responses. user_router.js Replace logic with calls to new lib * user_token.js Add jsdoc definition for return type and format function. user_router.js Remove unnecessary comment. * user_token.js More jsdoc definition; Add validation for collection token document required fields. user_token.test.js Add preliminary unit tests for static methods. * CMakeLists.txt Add new unit tests to build. user_token.test.js Modify naming to match convention. * CMakeLists.txt Fix variable get. user_token.js Fix export. * user_fixture.js Add new user for get/token tests. user_router.test.js Add simple tests for get/token endpoint. user_token.js Fix naming for token document scopes field. user_token.test.js Changes for scope field bugfix. * user_router.js Formatting; Throw error if more than one token matches, add note about token type. * ClientWorker.cpp Address some TODOs and extraneous comments. DatabaseAPI.cpp Remove TODOs. SDMS_Auth.proto Remove unused field. * user_token.js Update formatUserToken to always return object values. DatabaseAPI.cpp Add note on possibly missing field. user_token.test.js Update tests to check for new expected values. * user_router.js Clean up some comments for clarity. datafed-ws.js Formatting. * ClientWorker.cpp Rewrite comment regarding mapped token refresh. * user_token.js Formatting. * CHANGELOG.md update for feature * user_router.js Re-introduce accidentally removed `globus_collection` object. * CMakeLists.txt Remove comment about necessity * Add collection_type and collection_id to dat/put task state * support.js Update getAccessToken method to work based on collection information, JSDoc. tasks.js Include context required in call to getAccessToken, add comment on refresh. TaskWorker.cpp Identify where changes will be reflected. * Update token lookup logic to use `byExample`, add test case for missing Globus collection. Add globus_coll fixture. * SDMS_Auth.proto Change UserAccessTokenReply needs_consent to optional field. * user_router.js Update token/get to default to start consent flow when collection tokens are present. user_router.test.js Update test from error to needs_consent. * Formatting changes. * SDMS_Auth.proto Add new fields to DataGetRequest * Begin refactor of token decision logic. * Address bugs in fetching and mapping data, make unit tests pass. * globus_token.js Match other models for get * tasks.js Pull in new logic for determining tokens, replace tokens; Needs to be verified. user_token.js Add new format function for compatibility with transfer doc replacement. * DatabaseAPI.cpp Sane serialization of json body for taskInitDataPut. TaskWorker.cpp Comments around work items. * DatabaseAPI.cpp Sane serialization of json body for taskInitDataGet. * ClientWorker.cpp Stub out required changes for consent flow when creating tasks * ClientWorker.cpp More thorough consent flow for procDataPutRequest, stub on needs_consent * tasks.js Throw error when initializing data put * tasks.js Format error throwing. ClientWorker.cpp comment out potentially unnecessary code. * user_token.js Add exists method to abstract check. tasks.js User exists method when checking token. * user_token.js JSDoc typing * tasks.js Add more required fields to taskRunDataPut for refresh in TaskWorker. * tasks.js Add collection_id to params in taskRunDataPut for refresh in TaskWorker. TaskWorker.cpp Refresh conditionals * DatabaseAPI.cpp Update merged devel changes to address some leftover code. * DatabaseAPI.cpp Add collection specification to get request. * DatabaseAPI.cpp whitespace. ClientWorker.cpp Clean up unused code. user_router.js Switch to checking token existence through standard API. * user_token.js Add comment about type return. data_router.js Do validations at router level for user collection token relationship. tasks.js Remove validation from logic level; make dataGet mirror dataPut; Updates to naming and params structure. * ClientWorker.cpp Revert to minimize diff. TaskWorker.cpp Remove unnecessary TODO; move set client for refresh in transfer tasks. * models/ JSDocs, formatting, make token fetches follow defined model. user_token.js JSDocs and typing. * user_token.js Cover case where collection does not exist. * Small changes for UI detection of collection type * fix epview call for UI changes, add list view change to react appropriately to needing consent according to current code * extract ep view logic to function for either path to utilize * small changes and notes for UI updates * UI search based on path, not ID. camelCasing * TaskWorker.cpp small fix to only enforce requirement of additional refresh fields when token is transfer token. * add params for dat/get on UI * task.js Fix bug where client is incorrectly referenced. * Add user model tests. Extract DataFedOAuthToken.js from user_token.js for reusability. * Add globus collection model tests. * Add globus token tests. Add fixtures to support globus token testing. Make all model properties static for iteration purposes. Utilize constructors for typing. * Add user token tests. Make non-existent user throw an error when building user tokens. * Change error to be not found * Formatting changes * Remove unused changes in support.js getAccessToken * Changelog update, update comments, remove log. --------- Co-authored-by: Anthony Ramirez <[email protected]> * Add small fix for storeCollectionId (#1341) * Add small fix for storeCollectionId * move todo comment --------- Co-authored-by: Anthony Ramirez <[email protected]> * Fix bug with playwright (#1343) * Fix bug with playwright install for end to end web test --------- Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * [DAPS-1330] Address Download Extension Transfer (#1340) * [DAPS-1337] Refactor GET and Put mode * [DAPS-1337] Clear consent issue * [DAPS-1337] Correct bug * [DAPS-1337] Add Dir mode path logic update * Parse md json strings (#1347) * Parse md json strings * parse execQuery params * move to direct only * make params an object * remove console log --------- Co-authored-by: Anthony Ramirez <[email protected]> * [DAPS-1349] Provenance Capture Update Bug (#1350) * [DAPS-1349] Return logic to original check * [DAPS-1349] version * [Release] February 2025 (#1352) * updated versions for release * Trigger rebuild * Adjust deployment version number * Fix Version month * Update Version.cmake * removed leading zero --------- Co-authored-by: JoshuaSBrown <[email protected]> Co-authored-by: Joshua S Brown <[email protected]> * Add .venv/ to gitignore (#1335) * [DAPS-1388] Add GCP Support (#1392) * [DAPS-1388] Add endpoint model, Add endpoint model, unify seperate collection logic, endpoint validation check, Add endpoint query validations, next is token * [DAPS-1388] Add tests for model * [DAPS-1388] PR comments * Update web/static/components/transfer/transfer-endpoint-manager.js Co-authored-by: Joshua S Brown <[email protected]> --------- Co-authored-by: Joshua S Brown <[email protected]> * Add missing python module (#1404) * Set reasonable default that will help with filling in repo form for core t… (#1400) * Set reasonable default that will help filling in repo form for core to repo communication in compose file * Update scripts/compose_generate_env.sh Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Set appropriate default when building compose image --------- Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Add documentation describing how to test the foxx microservices unit … (#1393) * Add documentation describing how to test the foxx microservices unit tests * Update testing.rst * Note on database version, variable definition and usage when running arangodb version described, and steps to run unit test numbered. * Fix ci build (#1390) * updated requirements * updated requirements * updated protobuf submodule * update unit test ci version * updated protobuf version * updated setuptools version * fixed condition * changed where packages are installed * used python3.11 to create the virtual environment instead of latest * reverted protobuf version * testing specificying version * removed pyvenv in ci job for consistency * installed python3.11 in dependencies docker file * added missing -y flag * removed unification of install scripts * added missing python3.11 install * updated ci job to install python3.11 * changed installed python version to 3.9 since protobuf does not officially support 3.11 * changed installed python version to 3.9 since protobuf does not officially support 3.11 * missed version * updated includes for newer gcc versions * updated versions * updated nlohmann json * updated json schema version * changed library search path * hopefully fixed json dep issues * updating function signature to match newer version of base class * updated protobuf * updated protobuf and cmake * downgraded cmake * fixed protobuf version * fixed protobuf version * 1398 pin python version (#1405) * Pin python version * fixed incorrect path * Switch to using .tar file install of libsodium (#1414) * 1413 libsodium build refactor (#1415) * Switch to using .tar file install of libsodium * Switch bad option in wget command from -C to -P * Update scripts/dependency_install_functions.sh * Update scripts/dependency_install_functions.sh * Update dependency_install_functions.sh Libsodium folder version number. * Update dependency_install_functions.sh Make paths explicit. * cleaned up comments * Update scripts/dependency_install_functions.sh Co-authored-by: Joshua S Brown <[email protected]> * Update cmake/JSONSchema.cmake Co-authored-by: Joshua S Brown <[email protected]> * Update scripts/dependency_install_functions.sh Co-authored-by: Joshua S Brown <[email protected]> * Update cmake/JSONSchema.cmake Co-authored-by: Joshua S Brown <[email protected]> * add changes from review * Changed install scripts to be consistent with new python installation method (#1417) * changed install scripts to be consistent * added sudo check * add apt sources check --------- Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: nedvedba <[email protected]> * Fix regression (#1428) * Fix docker logs output in end-to-end tests (#1426) * Improve serialization randomization (#1427) * Increase serialization randomization pause heuristic - 6 seconds is not long enough to register running pipelines. * improve serialization * Upgrade formatter (#1440) * Update action for CPP and Python formatter * 1437 fix zmq inproc bind order (#1438) * Reorder zmq bind and connect calls to prevent undefined behavior when using INPROC * Make sure zmq messages are closed when exception is encountered * Make correction to socket name * Initialize cmd call * Add missing include * Allow looping over containers if there is more than one. (#1446) * 1445 docker logs multiple containers (#1447) * Allow looping over containers if there is more than one. * Fix multipline comment * Fix conflicting dependency install flags (#1444) * [DAPS-1408] Provenance Visual Management Lint (1/2) (#1431) * [DAPS-14xx] Move files over and move out svg * [DAPS-1408] Provenance Visual Management (2/2) (#1419) * [DAPS-14xx] Base * [DAPS-14xx] Add styling and tooltips * [DAPS-14xx] Add node and label customization * [DAPS-14xx] Add editor modal on right-click. Draggable model * [DAPS-14xx] Revert * [DAPS-14xx] Seperate files, update styles * [DAPS-14xx] simplify feat * [DAPS-14xx] Expand mocha tests, prettier * [DAPS-14xx] Update checkout version * [DAPS-14xx] Add todo * [DAPS-14xx] Update tests, consts, fix tooltip * [DAPS-14xx] Base: [DAPS-14xx] Address collapse, expand, hide * [DAPS-14xx] THEME, address comments * [DAPS-14xx] Zoom * [DAPS-14xx] JSDOC * Update web/static/jquery-ui-dark/datafed.css Co-authored-by: Joshua S Brown <[email protected]> * Update web/static/jquery-ui-dark/datafed.css Co-authored-by: Joshua S Brown <[email protected]> * Update web/static/jquery-ui-dark/datafed.css Co-authored-by: Joshua S Brown <[email protected]> --------- Co-authored-by: Joshua S Brown <[email protected]> * [DAPS-1395] Address Memory Leaks in Core Server (#1424) * Add missing virtual destructors * Fix ZeroMQ INPROC and TCP context * Add memory tests to CMakeLists.txt as an option * Add protobuf library shutdown to unit tests for memory cleanup * [TASK] Update tests and fixture (#1454) * [DAPS-1331] Collection ID Updated on restart (#1468) * [DAPS-1331] Modified the script to only delete and recreate guest collections when the base path actually changes * [DAPS-1331] Add base path logic * [DAPS-1331] Update guest collection file * [DAPS-1331] Fix base path caching logic in should_recreate_guest_collection function to recreate by default when no cached path is available * [DAPS-1331] Add tests * [DAPS-1331] Revert Gitlab CI * [DAPS-RELEASE] * [TASK] Remove icons from labels (#1489) --------- Co-authored-by: Anthony <[email protected]> Co-authored-by: Anthony Ramirez <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: AronPerez <[email protected]> Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: par-hermes <[email protected]> Co-authored-by: nedvedba <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Theo Beers <[email protected]> * [DAPS-1625] - user id map for session key josh (#1644) * [DAPS-1625] fix bug in session and transient keys. --------- Co-authored-by: AronPerez <[email protected]> * [TASK] Correct 2 spaces to 4 for YML (#1640) * fix: merge conflict changes that were missed. --------- Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: Anthony <[email protected]> Co-authored-by: Anthony Ramirez <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: par-hermes <[email protected]> Co-authored-by: nedvedba <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Theo Beers <[email protected]> * [DAPS-1585] [Dependencies] update: upgrade ssl dependency. 3.2.5 (#1646) * Staging to devel update (#1657) * Update devel from staging * [DAPS-1605] fix install_foxx.sh - split ssl_args (#1623) * fix(install_foxx): remove ssl_args argument it is not a valid flag. * Update devel from staging (#1649) * [DAPS-1585] [Dependencies] update: upgrade ssl dependency. 3.2.5 (#1646) * Staging to devel update (#1657) * Update devel from staging * [DAPS-1605] fix install_foxx.sh - split ssl_args (#1623) * fix(install_foxx): remove ssl_args argument it is not a valid flag. * [DAPS-1651] bug compose env generator (#1656) (#1658) * [DAPS-1651] fixed bug in compose env generator (#1656), compose_generate_env.sh script was not reading existing values correctly. * Adding the logger functions for future PR's (#1675) * feature: Implemented logging functions * [DAPS-1659] remove dependencies install scripts (#1660) * refactor: remove all scripts related to dependencies from DataFed repo * feature: update DataFedDependencies submodule and move ground truth of requirements.txt to DataFedDependencies. * 1669 feature support core service protobuf message with repo types (#1670) * 1671 daps feature foxx add repository and execution strategy types (#1672) * update: DataFedDependencies to 57483e1cd4eac9d84162dd7202e72fe353728361 * Update datafed dependencies (#1677) * refactor: remove remaining occurences of zeromq system secret. (#1661) * [DAPS-1678] refactor split error codes from foxx support.js and move to lib/error_codes.js (#1679) * [DAPS-1522] User router logging improvements (#1629) * style: Removed non helpful logs from tasks.js * fix: reverted protobuf to match devel (a9b006) * refactor: Refactoered the user_router to have a first pass of standardized logging (needs more testing) * style:Fomratted with prettier * refactor: changed correlation id within logs to use req.headers['x-correlation-id'] instead of just having placeholder text * chore: Auto-format JavaScript files with Prettier * refactor: First pass of logging within user_router.js * refactor: last minute changes * chore: Auto-format JavaScript files with Prettier * Refactor: Added second pass of logging to user router * Forgot to also add the new file * chore: Auto-format JavaScript files with Prettier * chore: Auto-format JavaScript files with Prettier * refactor:Made final adjustments to logging within user router * chore: Auto-format JavaScript files with Prettier * refactor: replaced undefined with null for appropriate areas; made slight changes to some log output to obfuscate sensitive data * refactor: Fixed spacing within logs; Removed unnecessary logging * chore: Auto-format JavaScript files with Prettier * chore: Auto-format JavaScript files with Prettier * style: Removed non helpful logs from tasks.js * fix: reverted protobuf to match devel (a9b006) * chore: Auto-format JavaScript files with Prettier * refactor: Fixed spacing within logs; Removed unnecessary logging * chore: Auto-format JavaScript files with Prettier * chore: Auto-format JavaScript files with Prettier * Style: Corrected status' on logs Co-authored-by: Joshua S Brown <[email protected]> * refactor:Second pass of user_router logging * refactor: Removed temporary logger file * refactor:removed external/protobuf * refactor: Final touches for logging * chore: Auto-format JavaScript files with Prettier * refactor: Cleaning up PII issues * refactor:Final checks, changed /view's extra output * Submodule update * refactor: Commited all reviewed changes * chore: Auto-format JavaScript files with Prettier --------- Co-authored-by: Joshua S Brown <[email protected]> * refactor: adjust validation.js swap g_lib with error_code require rem… (#1691) * refactor: adjust validation.js swap g_lib with error_code require remove circular dependency from validation.js by removing validateRepositorySupportsDataOperations Co-authored-by: Aaron Perez <[email protected]> * [DAPS-1692] - CI, End-to-end web tests, fix flaky test (#1693) * [DAPS-1694] refactor - Foxx move permissions functions from support.js to lib/permissions (#1695) * [DAPS-1685] Feature compose enable arangodb ssl (#1687) * [DAPS-1700] - [CI] - fix: limit arangodb job output to last 3 hours. (#1701) * [DAPS-1676] Feature - foxx arango add factory for repositories for metadata and globus (#1697) Co-authored-by: Aaron Perez <[email protected]> * [DAPS-1718] - Web, Core, Python Client - Protobuf ExecutionMethod enum, add RepoAllocationCreateResponse (#1719) * [DAPS-1713] - Core, Web, Python Client, refactor: protobuf, allow optional fields when creating repo to support metadat… (#1714) * [DAPS-1715] - Core, refactor: make path, pub_key, address, endpoint optional in repoCreateRequest (#1716) * [DAPS-1705] - Foxx, feature: integrate metadata globus factory repo router create (#1706) Co-authored-by: Aaron Perez <[email protected]> * [DAPS-1688] - Update dependencies, Crypto libssl switched to version 3 globus_sdk version pinned (#1689) * [1729-DAPS] - bug ci, downstream datafed dependencies pipelines are building the container image from incorrect sha (#1732) * [DAPS-1711] - feature foxx standardize repo response schema (#1712) * [DAPS-1725] refactor: remove confusing apache conf file. (#1728) * [1707] Update Web Dependencies Before Install (#1709) Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: JoshuaSBrown <[email protected]> * [DAPS-1522] - feature, foxx, task router logging improvements (#1648) Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: JoshuaSBrown <[email protected]> * [DAPS-1522] - feature, foxx, query router logging improvements (#1627) Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: JoshuaSBrown <[email protected]> * [DAPS-1735] bug: remove duplicate user_router test (#1736) * [DAPS-1731] - Feature, scripts, compose - add scripts to generate globus credentials for web service (#1731) Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * [DAPS-1725] - refactor tests mock core server centralized (#1726) * [DAPS-1741] Update: native client id in intialize_globus_endpoint and globus_clea… (#1741) * [DAPS-1745] - scripts fix: account for nested client credentials. (#1746) * [DAPS-1725-2] - tests, fix - centralized mock core service libraries fixed (part 2) (#1747) * [DAPS-1742] - refactor script replace os.path.join with urllib.parse.urljoin (#1744) * [DAPS-1749] refactor: set cmake policy to silence noisy warning. (#1750) * [DAPS-1522] - foxx feature tag router logging improvements (#1734) Co-authored-by: Joshua S Brown <[email protected]> * [DAPS-1378] - web, bug: fix mapping of multiple globus accounts. (#1753) * [DAPS-1756] - scripts, foxx, fix: add retries and connection check to install_foxx.sh script. (#1757) * [DAPS-1522] Version Router Logging Improvements (#1758) * [DAPS-1737] - compose, refactor compose cleanup arango ssl env variables (#1765) * [DAPS-1766] - fix python client provisioning job * [DAPS-1663] - Feature, Core Service, adding Correlation ID to Logging (#1704) Co-authored-by: JoshuaSBrown <[email protected]> Co-authored-by: Joshua S Brown <[email protected]> --------- Co-authored-by: Joshua S Brown <[email protected]> Co-authored-by: AronPerez <[email protected]> Co-authored-by: Anthony <[email protected]> Co-authored-by: Anthony Ramirez <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: par-hermes <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Theo Beers <[email protected]> Co-authored-by: JoshuaSBrown <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Polina Shpilker <[email protected]>
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* [DAPS-1585] - update: dependencies, upgrade ssl dependency. 3.2.5 (#1646) * [DAPS-1605] - fix: scripts, install_foxx.sh by splitting ssl_args (#1623) * [DAPS-1651] - refactor: scripts, compose, univify treatment of env variables in compose env generator (#1656) (#1658) * [DAPS-1675] - feature: foxx, adding the logger functions for future PR's (#1675) * [DAPS-1659] - refactor: scripts, remove dependencies install scripts (#1660) * [DAPS-1670] - feature: common, core, repo, python_client, web, allow passing repo types in protobuf messages (#1670) * [DAPS-1671] - feature: foxx, add repository and execution strategy types (#1672) * [DAPS-1661] - refactor: compose, scripts, remove remaining occurences of zeromq system secret. (#1661) * [DAPS-1522] - refactor: foxx, user router logging improvements, remove non helpful logs from tasks.js (#1629) * [DAPS-1691] - refactor: foxx, adjust validation.js swap g_lib with error_code require rem… (#1691) * [DAPS-1692] - tests: ci, End-to-end web tests, fix flaky test (#1693) * [DAPS-1694] - refactor: foxx, move permissions functions from support.js to lib/permissions (#1695) * [DAPS-1685] - feature: compose, enable arangodb ssl (#1687) * [DAPS-1700] - fix: ci, limit arangodb job output to last 3 hours. (#1701) * [DAPS-1676] - feature: foxx, arango add factory for repositories for metadata and globus (#1697) * [DAPS-1718] - feature: web, core, python client, Protobuf ExecutionMethod enum, add RepoAllocationCreateResponse (#1719) * [DAPS-1713] - refactor: core, web, python client, protobuf, allow optional fields when creating repo to support metadat… (#1714) * [DAPS-1715] - refactor: core, make path, pub_key, address, endpoint optional in repoCreateRequest (#1716) * [DAPS-1705] - feature: foxx, integrate metadata globus factory repo router create (#1706) * [DAPS-1688] - update: dependencies, core, repo, authz, gcs, Crypto libssl switched to version 3 globus_sdk version pinned (#1689) * [DAPS-1729] - fix: ci, downstream datafed dependencies pipelines are building the container image from incorrect sha (#1732) * [DAPS-1711] - refactor: foxx standardize repo response schema (#1712) * [DAPS-1725] - refactor: remove confusing apache conf file. (#1728) * [DAPS-1707] - update: dependencies, web, update web dependencies before install (#1709) * [DAPS-1522] - refactor: foxx, task router logging improvements (#1648) * [DAPS-1522] - refactor: foxx, query router logging improvements (#1627) * [DAPS-1735] - bug: foxx, remove duplicate user_router test (#1736) * [DAPS-1731] - reature: scripts, compose, add scripts to generate globus credentials for web service (#1731) * [DAPS-1725] - refactor: tests, mock core server centralized (#1726) * [DAPS-1741] - update: scripts, native client id in intialize_globus_endpoint and globus_clea… (#1741) * [DAPS-1745] - fix: scripts, account for nested client credentials. (#1746) * [DAPS-1725-2] - fix; tests, centralized mock core service libraries fixed (part 2) (#1747) * [DAPS-1742] - refactor script replace os.path.join with urllib.parse.urljoin (#1744) * [DAPS-1749] - refactor: cmake, set cmake policy to silence noisy warning. (#1750) * [DAPS-1522] - refactor: foxx, feature tag router logging improvements (#1734) * [DAPS-1378] - fix: web, mapping of multiple globus accounts. (#1753) * [DAPS-1756] - fix: scripts, foxx, add retries and connection check to install_foxx.sh script. (#1757) * [DAPS-1522] - refactor: foxx, Version Router Logging Improvements (#1758) * [DAPS-1737] - refactor: compose, cleanup arango ssl env variables (#1765) * [DAPS-1766] - fix: ci, python client provisioning job * [DAPS-1663] - feature: core Service, adding Correlation ID to Logging (#1704) Co-authored-by: Aaron Perez <[email protected]> Co-authored-by: AronPerez <[email protected]> Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> Co-authored-by: nedvedba <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Austin Hampton <[email protected]> Co-authored-by: Blake Nedved <[email protected]> Co-authored-by: Polina Shpilker <[email protected]>
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Ticket
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How Has This Been Tested?
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Summary by Sourcery
Bug Fixes: