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Changelog

9.61.3 (2024-10-30)

Bug Fixes

  • added null handler for dataset mapping getter (7fbf1a8)
  • null handler for default model format in spec and form and whitespc (c4eea35)
  • update format name in spec test (f2731de)
  • update upload model test for proper test fixture (7d16406)

9.61.2 (2024-10-16)

Bug Fixes

  • add needed imports for hpc singularity builder unit test (5f8bfba)
  • throw exception with error message if fail to process sedml (65efa6a)

9.61.1 (2024-10-02)

Bug Fixes

  • update download artifact version in deploy workflow (469581d)

9.61.0 (2024-10-02)

Bug Fixes

  • added run biosimulations handler (bfcfcf7)
  • const over let for lint (485e449)
  • finally updated and fixed custom project param setters (df42912)
  • remove offending line for lint (83742d1)
  • remove unused imports for lint (fde31bb)
  • update project forms (256a039)
  • update to create project handlers (5441da5)
  • update to custom rerun (e48826c)
  • update to new project submission handler (05e4554)
  • updated spec (ab94c82)
  • upgraded upload artifact action version and rem log (578462d)

Features

  • added download of custom archive (ba7f976)
  • added model verification component for site utils (2e2b1c2)
  • added placeholder verification content (e3379fa)

9.60.1 (2024-09-02)

Bug Fixes

  • accommodate undefined image url array in create project from sbml (0d3b834)

9.59.0 (2024-04-25)

Bug Fixes

  • accessed sed model changes (ae573c0)
  • added combine archive return (c88f40e)
  • added config service injector for calls (a2aecda)
  • added http client to mockup (dbc19b1)
  • added objects to custom spec (840dcfd)
  • added providers remaining to customize simulation (384fc05)
  • added snackbar to spec (1c4fff1)
  • removed console for sonarcloud logging detect (54bf7e5)
  • revert iframe (a469e5f)
  • updated disable eslint for line (eb65fe3)
  • updated method to receive sim params (ee6f468)
  • updated providers mockup for custom (5c25a27)
  • updated sim override handler and checkbox (aa20214)

Features

  • added customize component to platform (98f76c7)
  • copied content from dispatch (7c10895)
  • implemented model changes form in custom component (6ab77c3)
  • refactored custom form and optional renders (7d35b45)
  • updated archive creation handler (fc6b5b7)

9.58.0 (2024-04-11)

Bug Fixes

  • added api target (4feafcb)
  • added catch clause (4e2b106)
  • added catch to nav (5215b42)
  • added commonjs mapping (86a8c23)
  • added configService provider to shared status service test bed (c523cc8)
  • added dispatch spec handler (b00712d)
  • added download (1a0cf0e)
  • added enumeration indices to service implementation in dispatch (fed64e0)
  • added esm use (22c47a9)
  • added esmodule interop to services ts spec config (3a80fde)
  • added formatted simulation to spec (6dacfa5)
  • added handler specs (b7b76a2)
  • added http handler (caca0d0)
  • added hydration to handler (b8aa6ae)
  • added jest config (a9d35a6)
  • added metadata handler (cf1201e)
  • added onInit trigger for utc params (2cd07af)
  • added provider for shared service spec (b3ccd36)
  • added refactor (cd3528b)
  • added scope to eslint (273da8b)
  • added semantic commits to gitignore (6cd4d15)
  • added setter to constructor (f938bc0)
  • added transform ignore (cbef444)
  • added transform ignore to api spec (785851a)
  • adjusted handler (ca5090f)
  • adjusted sim run controller spec (f053bef)
  • adjusted ts jest in preset (e7b696a)
  • auto stash before merge of "add-editor" and "origin/add-editor" (237a983)
  • changed namespace for shared service test (8674abe)
  • created test-setup for jest (620c905)
  • imported matcard module in test for platform overview (d1bbfaf)
  • refactor (cd3c726)
  • refactored shared sim service uses to absolute imports (e89d7f7)
  • rem types from api tsconfig (21b8ee9)
  • removed exports from shared (b33b85f)
  • removed ext from preset jest (d5e2188)
  • removed hidden simulator card added rerun handler and cleaned load (8a3afad)
  • removed log and added config service provider to sim spec (b39c72b)
  • removed module from tsconfigs (02ee0b5)
  • removed null return (6ab97d8)
  • removed optional operator in component dec (bcd19e4)
  • removed self provider from shared spec (f485d73)
  • removed shared ui content (9799e29)
  • removed unused on init (de64a45)
  • revert change (6f373e8)
  • revert poetry config (163daac)
  • revert pyproject in simdata (8360499)
  • revert semantic commit (69ab7e9)
  • revert to working specs (5833fef)
  • revert tsconfig and absolute import (e2996ca)
  • revert workflow (11b970c)
  • run app spec (0299db7)
  • sed specific implementation (293090d)
  • shortcut route (eefc276)
  • ts config (5ea692d)
  • updated allowed commit temp (5fc3092)
  • updated config (e9f58ce)
  • updated css and array instance name for builder (ad61109)
  • updated es module target for api spec (f4cedc3)
  • updated files for failing tests (73c580b)
  • updated files subscription for sbml setter (247b172)
  • updated global jest and api config (1e21516)
  • updated metadata addition to archive creation (28e1f6a)
  • updated nx cloud in package json (b7abbca)
  • updated parameters form interface for n string params (420d571)
  • updated poetry config to include flask option in connexion (0895df2)
  • updated project introspection form params (c55a47a)
  • updated shared service (f8d084e)
  • updated shared service spec for storage and other injectables (7516e66)
  • updated shared service tsconfig to include es2020 (2ae1d10)
  • updated simulation shared service to include proper providers (f4d607d)
  • updated spec file for shared sim service (c63f52f)
  • updated ts spec config to include ecma script module (c3b12bb)

Features

  • added activated route to create project (f3ca9a3)
  • added biosimulators-utils to poetry config (b116d41)
  • added changes access (b581906)
  • added correct angular template getter data to html and kept mock (dc562e8)
  • added form builder implementation in dispatch (aa1e478)
  • added image files to project (d70d680)
  • added non sbml and supported handler (f4ae688)
  • added observable to rerun (464be7b)
  • added parameter change form on archive submit (f7b301a)
  • added post sed doc method (a0712ce)
  • added project metadata file (37b9b59)
  • added service method for platform (e6aef1e)
  • added shared form (b04abb2)
  • added sim and model form data interfaces in dispatch (658a207)
  • added simulation service method (016ddfe)
  • copied content for shared (8aa5213)
  • copied content from model changes (da069bb)
  • copied full service from service (6c24041)
  • correct implementation of service (0f247c5)
  • created and implemented rerun custom overview btn in platform (c401b0d)
  • created shared service file and updated shared datamodel (1c29df2)
  • extracted full params (8d40ad2)
  • ported utc params (73b3763)
  • provided url transform to reroute dispatch runs to biosimulations (f0a24bb)
  • reformatted code and implemented third solution type to dispatch (3e167bb)
  • request now working (fc5190f)
  • update setters and add changes getter (1d645ec)
  • updated click handler savepoint (2846901)
  • updated introspection (5215b73)
  • updated project metadata in view to handle images (79bb1af)
  • updated sim service with shared (f137f83)
  • updated utc params (b5962b5)

9.57.0 (2024-02-02)

Features

9.56.1 (2024-02-02)

Bug Fixes

  • removed conditionals to allow for all plots to render (eacb23c)
  • updated visualization dec in platform runs view (fb3f5cb)

9.56.0 (2024-02-01)

Bug Fixes

  • added header to smoldyn test (a707889)
  • added smoldyn testing method (0052fa6)
  • adjusted transparent border for hover topbar (a381e3c)
  • commented-out unused future dep (aa77170)
  • reimplemented breaking changes (20eb70c)
  • reimplemented python version from before (d2f9128)
  • removed processes and simularium content from pyproject.toml (c71727d)
  • removed smoldyn test to appease ci (f9b1ee0)
  • reverted simulation runs view endpoint until consolidation (8dfbe18)
  • ui: adjusted hover menu style params (1829758)
  • updated biosimularium version and lock file in pyproject (319f505)
  • updated poetry lock (8bc4b8e)
  • updated poetry lock in combine (6f351de)
  • updated pyproject (1c64e99)
  • updated pyproject and lock (7c1b939)
  • updated pyproject for bumped python version (1e210a3)
  • updated run handler simularium dec (1d962c2)
  • updated run handler to properly bundle simularium output (2215b5f)
  • updated smoldyn installer for ARM (3487f2d)

Features

  • added auto checkbox functionality to email field in dispatch form (e8d0c79)
  • added helper scripts (c67350f)
  • added simularium generator to run handler (d606faa)
  • added smoldyn model file to test fixtures (cd67f28)
  • adjusted simularium implementation (7ccd7b7)
  • autocheck for academic use in dispatch form (68f28a2)
  • implemented component rendering for simularium files (e595bca)
  • updated config for new sim (3524913)
  • updated python version and lock in combine (b5bc316)
  • updated run implementation (177f7c1)

9.55.5 (2024-01-30)

Bug Fixes

  • use async DynamicModule with config to initialize simdata-api path (2631de5)

9.55.4 (2024-01-29)

Bug Fixes

  • correct usage of NdArray in results.service (f2e8b22)

9.55.3 (2024-01-29)

Bug Fixes

  • restore path simdata.api.biosimulations.dev (77eb69f)
  • root logger configuration fixed (c3decc1)
  • support both outputs and contents dirs for reports.h5 (b61b308)

9.55.2 (2024-01-27)

Bug Fixes

  • add CORS support for simdata-api (49cf965)
  • lint error fixed (c9926b2)
  • use FastAPI import for CORS to guard against future FastAPI changes (06f5de6)

9.55.1 (2024-01-26)

Bug Fixes

  • disable broken UpdateSitemaps step of Continuous integration (2599e84)
  • disable updatesitemaps again (88e305d)
  • rename simdata.api.biosim to data.biosim to reuse tls cert and path (4afcd0e)
  • restore api.biosimulations.dev/health/dataService endpoint (7af2be4)
  • roll back unneeded upgrade of openapi-generator npm package (a692aeb)

9.55.0 (2024-01-26)

Bug Fixes

  • accommodate missing attributes in hdf5 (7036859)
  • add hdf5 file metadata endpoint to simdata-api (f37d8ed)
  • add health endpoint to simdata-api (e53ad36)
  • added HDF5 visitor to extract metadata and added uri and id (477710e)
  • added helpful S3 functions to upload/download/list files (2fd4afd)
  • added mypy and coverage dependencies for dev tooling (414aa87)
  • added uri and id to HDF5File dataclass (d937ef9)
  • allow in-place testing of simdata-api Docker container (f0df1d1)
  • async simdata-api endpoints via aiofiles and aiobotocore (07a2e15)
  • build option for simdata-api (a055a97)
  • cleaned up hdf5_utils to only work with local files (0a86f20)
  • decouple HSDS/HDF5 lib, remove HSDS upload, format simdata-api (435953d)
  • Docker env vars and skip tests if no credentials (68c6408)
  • done with first pass at results.service migration (21ea164)
  • fixed hdf5 attribute lookup logic (7b95e07)
  • fixed mypy typing errors (26819bd)
  • fixed naming in /libs/simdata-api/nest-client-wrapper (30c1817)
  • generated client has a mispelled variable (d3f31b1)
  • handle NotFound as 404, fast optimistic retrieval, better logging (c274966)
  • improve uvicorn invocation in Docker (e0ab507)
  • integrate dataset and modified-date simdata-api endpoints (de5c8fe)
  • introduce logging into simdata-api (4d8f404)
  • lazy ETL from S3 hdf5 to S3 zarr/n5 for array or metadata requests (1807354)
  • more minor linting errors (62f421b)
  • move /libs/hsds/client to /libs/simdata-api/nest-client-wrapper (e7a01dc)
  • read/write zarr2/zarr3/n5 to gcs (Google S3) and local files (380647a)
  • read/write/test in N5, Zarr2, Zarr3 using TensorStore locally (8c22e26)
  • remove all remaining references to HSDS in repo (ab7a0b4)
  • removed optional null values from hdf5 metadata dataclasses (ba364a0)
  • removed unused /libs/simdata-api/nest-client-wrapper (will replace) (2190085)
  • rename dataset api endpoint to /dataset/{run_id}/data (322ac1e)
  • replaced HSDS getDatasets() (5b68363)
  • return dataset as numjs ndarray, add get_modified endpoint (8c5a078)
  • simdata-api docker build and lint errors (bc5eb7e)
  • simdata-api downloads h5 files from s3 and extracts datasets (674e021)
  • simdata-api generated api client syntax error (2212e93)
  • style lint errors and formatting in simdata-api (5001f89)
  • TensorStore s3 KvStore, use gcs which needs Google credentials (3126cfa)
  • update the actual slurm script to not upload to HSDS (7ce4aa1)
  • upgrade python to 3.11 (7ce43fe)
  • upgraded openapi-generator and forced spec to 3.0.3 to get types (2c42ac0)
  • use openapi-down-convert to properly produce OAS v3.0.3 spec (4f01f42)
  • validation of openapi specs failed with wrong filename (9ced0d3)

Features

  • add SimDataService as Typescript/NestJS API client for simdata-api (c081d30)
  • introduce simdata-api service to replace HSDS (7488f9c)

9.54.5 (2024-01-10)

Bug Fixes

  • added data to logging statements (f9cd643)
  • commented out hover description (0ce9089)
  • updated job error messages (8452f14)
  • updated process log message to include reason if fail (efd364e)
  • updated processor and complete to reflect logic (c8d961c)
  • updated structured log to include more extensive message (3ac6fc5)

9.54.4 (2024-01-06)

Bug Fixes

  • job status is now tolerant of Slurm Job HSDS upload retries (8d4fb56)

9.54.3 (2024-01-06)

Bug Fixes

  • missing space in bash script (1edf106)

9.54.2 (2024-01-05)

Bug Fixes

  • add jest test for sbatch template generation to verify syntax (3a97587)
  • more informative slurm script and always upload final rawLog.txt (1903607)
  • send final log file to server upon SIGTERM when job timeout happens (1f6fbf2)

9.54.1 (2023-12-31)

Bug Fixes

  • adjusted overflow for side bar content (68fb89b)

9.54.0 (2023-12-27)

Bug Fixes

  • added archive files pipe to correct project files component attrib (9609cad)
  • connected simulation run output pipe with dropdown (f04dc83)
  • externally-managed-environment error fixed with venv in Dockerfile (256cb13)
  • removed duplicate selector declaration (fc44fb3)
  • update (a3a505a)
  • updated package-lock (c038418)
  • upgraded sharp package to fix install error (b1d3a19)

Features

  • ui: moved simulation files dropdowns to spec tab and removed dwnld (e2f695f)

9.53.0 (2023-11-10)

Bug Fixes

  • added adjustments to agreement spec (6c4326d)
  • added imports and providers (3b3a543)
  • added storage to spec (c517ea4)
  • changed implementation class attribute name to appease ci (319a093)
  • declared correct tab index values for select and view viz tabs (7cd4bc4)
  • downgraded fix spelling version (21886f8)
  • re-used main in workflow spelling file (708d710)
  • reimplemented check spelling version change (e1f0150)
  • renamed unique method to appease CI duplication in dispatch (f7569cf)
  • specified stable version for check-spelling workflow (a63e70c)
  • updated agreement spec file to reflect markdown removal (ce6f5a2)
  • updated commits (db0b69c)
  • updated spec files for platform and dispatch overview (cc7b46c)
  • updated unique class names on components (26028d5)
  • updated viz display component declaration (1c20aa3)

Features

  • implementation of rerun button in dispatch overview for projects (6383769)
  • implemented run overview with rerun button in platform simulations (b9a155b)
  • implemented styles for overview spec containers (436ac77)

9.52.3 (2023-09-27)

Bug Fixes

  • adjusted file getter logic in simulators view component (f75505d)
  • adjusted simulator view layout (ad6dea2)
  • adjusted validation results tab in simulators view component (893f83d)

9.52.2 (2023-09-05)

Bug Fixes

  • adjusted browse simulations table styles (04e42bb)
  • adjusted details expansion panel order and pre opened rendering (192373d)
  • adjusted legend location (4e32ea1)
  • adjusted top margin of right col card in platform view (a4d86f5)
  • adjusted view plot legend and plot layout (002e89a)
  • continuity styling (fa02f0c)
  • implementation of two-way event and property binding for fragments (ecd2a6b)
  • removed fully unused drag implementation (5b00e89)
  • updated app footer heading color (31dcf16)
  • updated color of form steps card header (4f1d756)

9.52.1 (2023-09-01)

Bug Fixes

  • added blank target to dispatch simulators nav button (4c29e9e)
  • added top scroll to dispatch submit in platform and dispatch (c302429)
  • adjusted class for duplication (26d1921)
  • adjusted combinator to prevent duplication (f34799e)
  • adjusted dispatch simulation view styles (f068d3f)
  • adjusted layout of view and tab page styles (0efef0f)
  • adjusted simulation plot select view ui (9a7873d)
  • adjusted styles in overview and sim view (e4eb3bb)
  • adjusted tab page margins (9b65101)
  • adjustment to paging form component styles (b28ecb3)
  • adjustment to run view styles (d0bc5e2)
  • adjustment to tab page view and global styles (cf9bc6e)
  • adjustment to utils styles (de13b55)
  • adjustment to view files component (8042175)
  • adjustments to global and shared component styles (f011d1e)
  • adjustments to shared page component (b51d9f1)
  • adjustments to simulation log component (b64607b)
  • adjustments to simulation log layout (9996f9b)
  • adjustments to text page sidebar sections and children (959f994)
  • continuity styling for platform dispatch (5279fcb)
  • continuity styling for platform dispatch component (bb5f252)
  • continuity styling in platform simulation log component (8569f85)
  • created global multipurpose card header for cross repo continuity (ed353b1)
  • implemented mat-tab heading icons in platform (93c8679)
  • implemented updated dispatch global styles (11e4a43)
  • refactored class encapsulation and deleted unused heading (4c1630d)
  • refactored project metadata container width and styles (9f7e5b5)
  • removed blank target in platform browse (a96851e)
  • removed comment for code duplication (a13c727)
  • removed fit content height in sidebar (d667ac7)
  • removed re-run button temporarily (011c90f)
  • static positioning of eventual implementation called sidebar (a9a529d)
  • substantial simulation run page ui overhaul (fef30da)

9.52.0 (2023-08-30)

Bug Fixes

  • final adjustment to button color for continuity (b00f15b)
  • refactored footer button to be wrapped in relative anchor for click (3446436)

Features

  • ui: created + implemented global multipurpose flat button instance (fa4db17)

9.51.6 (2023-08-30)

Bug Fixes

  • try HSDS up to 40 times, sleep 5s to 15s between each (3b4bb2c)
  • try to upload to HSDS up to 20 times, 0-19 seconds between tries (fa1bd76)

9.51.5 (2023-08-29)

Bug Fixes

9.51.4 (2023-08-29)

Bug Fixes

  • update hsload args for h5pyd 0.14.1 to upload to HSDS from Slurm (6b08d5d)

9.51.3 (2023-08-28)

Bug Fixes

  • add comment to use when bypass test failure with approval (11ae9cb)
  • disable COBRApy and RBApy deploy tests until new Gurobi license (f87c3e2)
  • revert use of redundant review_dev_deployment_tests_environment (467ba14)
  • small text fix to force build and deploy (884561d)

9.51.2 (2023-08-28)

Bug Fixes

  • added matcard import to dispatch app (0c7850d)
  • added safe operator to handle undefined in tests during ci (76de168)
  • biosimulations opens to blank target for repo continuity (8795914)
  • imported card module (2234028)
  • imported mat card module in overview component file (f1b0848)
  • removed duplicated css declaration to appease ci (c3abb75)
  • removed overflow from y axis in dispatch form (19d02db)

9.51.1 (2023-08-24)

Bug Fixes

  • adjusted added app global style and removed (43e5395)
  • adjusted and added run simulations pointers and changed btn txt (c78829b)
  • adjusted button styles and color (c3443dc)
  • adjusted shadow dom class style height and removed unused container (fef3d99)
  • adjusted styles of nav buttons (4276ade)
  • adjusted styles of topbar items and removed unused (9dda677)
  • removed heading separator and home description container type (b329724)
  • removed text color styling and footer heading anchor (169e13c)

9.51.0 (2023-08-22)

Bug Fixes

  • adjusted endpoint of docs item (b305b8a)

Features

  • ui: adjusted home page wording in simulators app (403e4f5)
  • ui: implemented footer in platform mobile (d7724d2)
  • ui: implemented shared app footer component in dispatch app (7263c2d)
  • ui: implemented shared ui footer component and implemented cols (62bda34)
  • ui: moved shared footer from home to app comps in repo ui apps (f40437b)

9.50.1 (2023-08-18)

Bug Fixes

  • adjustment to component styles (16e9eb2)
  • adjustment to platform specific home page styling (13d1e5a)
  • adjustments to global simulators and dispatch styles (f267748)

9.50.0 (2023-08-18)

Bug Fixes

  • adjusted verbose feature dropdown on platform home (d9ccee6)
  • removed unused import (49aabde)

Features

  • ui: implemented color changing logic for simulators app hero (eb9c2c0)
  • ui: implemented logic to change nav button color based on app name (b1f0c96)

9.49.0 (2023-08-17)

Bug Fixes

  • added correct config pointer to home anchor href (aee5005)
  • adjusted tooltip description for tors button in dispatch (98ee754)
  • adjustments to various css files (469f9a9)
  • appended correct pointing to app route platform url value in tors (e72e3f1)
  • container declaration to global and global text color adjustment (e47550c)
  • removed unused docs button in place of utils component (05bc54d)
  • used link for browse reference in simulators home (afb9d57)

Features

  • ui: added docs button to shared utils btn component with styles (b036e84)
  • ui: added tool tip descriptor for non dropdown menu buttons (e419963)
  • ui: added tooltip delay to shared scope for reactive display (13555a1)
  • ui: added tooltip descriptor to dispatch biosimdb nav button (2fb6e26)
  • ui: added tooltip descriptor to platform biosim db button (8f31342)
  • ui: adjusted nomenclature of global stylings (b83ef2f)
  • ui: adjusted styles of dispatch app home page and hero (de09816)
  • ui: adjustments to contents and styles in dispatch and tors home (567e2e7)

9.48.2 (2023-08-14)

Bug Fixes

  • refactored and cleaned all shared component scss files (80759fe)
  • refactored component scss code to appease ci/cd (16f94c2)
  • refactored declarations and removed unused to prevent duplication (00bcbb3)
  • refactored for unused code and single line comments to appease ci (3c4861b)
  • refactored offending scss file in home teaser to appease ci (f8dd803)
  • removed comments and unused code to appease CI/CD (0dde49b)
  • removed unused and added correct import (f5995dd)
  • removed unused font type and comment in constructor (b0f3c80)
  • replaced material design getters with css var declarations (bbb947b)

9.48.1 (2023-08-13)

Bug Fixes

  • removed unused code in notice css file (7b4cc8a)

9.48.0 (2023-08-12)

Bug Fixes

  • added default values and adjusted attribute declaration (592a236)
  • added docs and validation fields to simulators config json (035606f)
  • adjusted accessibility of attributes and implemented app routes (cad32fa)
  • adjusted shared utils component and config implementation (7ef5784)
  • correct declaration of href in simulators app html (45a7d89)
  • implementation of routes and config in projex (54f928c)
  • implemented app routes instances for projex app in home component (c69f058)
  • implemented app routes object in app.component for parsing urls (b72310e)
  • implemented projex app routes instance in place of config in browse (3eb559c)
  • removed builtin attributes from component declaration (e9c3c6d)
  • resolved merge conflict using cli (51b11de)

Features

  • adjusted utils button class and altered implementations (5a48e87)
  • implementation of routerLink and appRoutes setters in simulators (e776d70)
  • implemented and adjusted shared utils button component (772ff26)
  • implemented approutes and new config values in dispatch components (158befb)
  • implemented new app routes instance globally for dispatch app (5adb8c2)
  • implemented new config values in platform app component (39ba353)
  • implemented new instance of app routes object globally in platform (9ebb4c0)
  • implemented new properties in config for dispatch and platform (2120dd8)
  • implemented shared utils button for projex and simulators apps (bfe5d20)
  • implemented shared utils button in dispatch (74e7ff0)
  • implemented specific declarations for routing (c691ea9)
  • imported and implemented app configured routes object in submods (78f9190)
  • ui: created and implemented shared utils to prevent duplication (44be764)

9.47.0 (2023-08-10)

Bug Fixes

  • added appropriate routerLinks and renamed link to more explicit href (074cb7e)
  • adjusted routing in projex (2918c2d)
  • changed mobile link pointer to local route (6e84362)
  • proper implementation of routing in projex to appease ci (9be2732)
  • renamed attribute implementation in app.components (8c828c2)

Features

  • implemented dropdown menu with local routes for platform hero (54e1b0a)
  • ui: implemented mobile footer in app component (e1bf0fd)

9.46.0 (2023-08-08)

Bug Fixes

  • added noop to simulators home spec due to encapsulation error (d10ea86)
  • added target to transition declaration (bc8fc63)
  • adjusted single line comments to appease CI (6f07744)
  • re-implemented Nooper to fix mistake (6668666)
  • removed duplicate display (e45968f)
  • removed duplicate transition property (4c83bd3)
  • removed mobile content for sep of concerns (668a036)
  • removed noop from test to appease ci (cdbb8e1)
  • removed target from binder href (b4b82d4)
  • renamed shorthand and removed duplicate declaration (32f5d61)

Features

  • ui: added binder ref to card and cleaned styles removing direct (baa288f)
  • ui: added getting started quick start guide to simulators landing (d7e7acc)
  • ui: added updated stylings and screen checking logic for mobile (58f468c)
  • ui: implemented docs card in simulators (51ba718)
  • ui: implemented updated mobile stylings and logic for dispatch (de58118)
  • ui: implemented updated mobile stylings and logic for platform (cef98bd)
  • ui: implemented updated mobile stylings and logic for simulators (2a5d075)

9.45.0 (2023-08-06)

Bug Fixes

  • added block comment and removed console log with template literal (a1dc8f4)
  • added correct internal routing to component (29e59b9)
  • added generic font family to appease CI (ca5544f)
  • added home container declarations and styles for CI (3692f4a)
  • adjusted link directives and removed unused components (03addba)
  • implemented mat card teaser sections and cleanup to appease CI (ae83650)
  • removed duplicate css declaration (e23da9f)
  • removed duplicate declaration and added standardized font size (8f8dabb)
  • removed duplicate topbar declaration (28ea40f)
  • removed single line comments and replaced non repo imports (ed4b257)
  • replaced single line comments with block comments and removed some (0a84683)
  • ui: added container for CI and adjusted tabular data button (339e890)
  • ui: implemented builtin default theme with css declarations in dis (3026e59)
  • ui: implemented default angular themes in simulators app (f58e711)
  • ui: implemented explicit setter for biosimulations icon component (c82b802)

Features

  • ui: added different home teaser images and correct paths (9f7bd67)
  • ui: added footer section and parent container to dispatch home (a71c91c)
  • ui: added tab page header and container with logic and styles (1718953)
  • ui: added updated home carousel images to local assets dir (f2bc8f4)
  • ui: implemented footer section in simulators home component (3ca11cf)

9.44.0 (2023-08-04)

Bug Fixes

  • added eslint comment for empty constructor and changed comment form (51f41f3)
  • changed appropriate namespace of image file for simulators (c60091a)
  • ui: added trigger logic to close menu on click directive (fffc135)
  • ui: removed shared component container for div (07f56a5)

Features

  • added updated png image to assets subdir (a06e258)
  • ui: added path of updated logo image to config.json in simulators (eed361d)
  • ui: added roboto font family to home section for continuity (58c422f)
  • ui: implemented mat cards for algorithms tab in view simulator (32ea82b)
  • ui: replaced shared components with mat card for continuity (eb7c48c)

9.43.1 (2023-08-03)

Bug Fixes

  • linting errors in combine-api handler (df00adf)
  • used correct env variable for S3 secret key (4df9cf9)

9.43.0 (2023-07-31)

Bug Fixes

  • added nowrap declaration to table container (c26ffd8)
  • removed commented-out css declarations to appease CI (f601e10)

Features

  • ui: added color selecting behavior to navigation component (cb2a93b)
  • ui: added color selection logic for apps (9d9e5a5)

9.42.0 (2023-07-28)

Bug Fixes

  • added correct local pointer routerlink to biosimulators button (dab2a19)
  • adjusted padding (152c6fe)
  • adjusted pointer for app routes test (c52f2a9)
  • adjusted pointer value for concat in setter for test (a23100c)
  • adjusted pointers in config (5915267)
  • changed external pointer of featured service (e28d547)
  • combined material icons import statement with fonts and removed un (ff106b6)
  • mult-line comments to single line to appease ci (6f613bc)
  • production site pointer in place of dev in dispatch config file (f53c9f8)
  • removed template literal from simulator component method (b92b885)
  • removed trigger id from hover open menu item in platform (8e7fd79)
  • toggled value in endpoint loader to use prod (3f899af)

Features

  • added rest api service and update text to home carousel (de6c2a7)
  • ui: combined simulation run with run metadata for clarity (6ddc2b2)

9.41.1 (2023-07-26)

Bug Fixes

  • removed linkClicked method from click event in hover open menu comp (7cca3c8)

9.41.0 (2023-07-21)

Features

  • implemented fully functional hero banner for dispatch app (4251747)
  • ui: adjusted browse runs header text (1a5ea08)

9.40.0 (2023-07-07)

Bug Fixes

  • added link to reprod center (261e50e)
  • hardcoded prod endpoint for dispatch app in dev stage and prod (f7facb1)
  • implemented explicit declaration of prod site pointer for dev runs (265cff3)
  • implemented more explicit logic for endpoint loader run handling (e8a366e)
  • removed unused color prop and removed comments from project colors (c7886b1)

Features

  • added teaser links to home-teaser component (2161deb)

9.39.1 (2023-07-06)

Bug Fixes

  • s3 import in combine-api and updated create-project unit tests (d4cd303)

9.39.0 (2023-07-06)

Bug Fixes

  • added const for toggling prod and dev in routing spec (59568af)
  • added endpoint handler method for toggling the use of prod dispatch (541d69d)
  • added flag to dropdown menu item background in css declaration (6878f74)
  • implemented variable to app routes spec to point correctly (2aacddb)
  • merge pull request #4723 from biosimulations/dispatch-fix-layouts (1789039)

Features

  • added generic handling methods for iterating over services (490ee99)
  • added reprod portal endpoint teaser text to featured component (8dcb247)

9.38.0 (2023-07-03)

Bug Fixes

  • added temporary nosonar comment to affected code (01d5d92)
  • codefactor apply fixes to commit 1950086 (026b6b3)
  • created and implemented combined observables datatype to avoid any (7e82bd6)
  • finished handling logic to include default axis layout (21e8329)
  • removed comment in home and reformatted comments in projects chips (803e735)
  • removed comments from view component to appease CI (0245689)
  • removed nosonar and commented out template literal log messages (a82ed70)
  • removed return duplicate and added explicit return type (d2b049a)
  • removed unused edit method that was causing sonarcloud errors (1950086)
  • removed unused method for sonarcloud code duplication (94bbf56)
  • removed unused methods and added explicit typing (f305663)
  • removed unused props and some any (16c6651)
  • used forEach implementation in place of traditional for loop (68bd734)

Features

  • added customized container for mobile screen viewport change (147ca2a)
  • added handset and tablet responsive design to view component (e4dffbb)
  • added logic for handling for swipe as click listeners in featured (0205a8e)
  • added mobile design to home teaser (2a0750e)
  • added mobile handling logic to home teaser component (bec5c9a)
  • added mobile teaser title handling for verbose titles and styling (50b00de)
  • added mobile-responsive design to home teaser carousel component (7269475)
  • added more mobile styling handling logic and removed used prop (4704e6d)
  • added optional range slider and toggling mat-radio buttons (672a37e)
  • adjusted async autoscroll logic with custom sleep method and swipe (42eac61)
  • adjusted plot legend position and added range slider (875435a)
  • complete implementation of projects-chips from projex in platform (8b24de8)
  • implemented mobile styling for home teaser featured component (377acdd)
  • implemented project view simulation profile page from -jex in plat (fc645e4)
  • implemented project-table files from projex in platform (e8300c6)
  • merge pull request #4722 from biosimulations/view-and-projects-to-platform (8565537)
  • remove dropdown in place of matToolTip for tors nav button w blank (a8a95ce)

9.37.0 (2023-06-27)

Bug Fixes

  • added NoopAnimationsModule to home and featured component spec file (4e88579)
  • removed rerun custom sim from featured carousel on home teaser (ad897a1)

Features

  • added routing logic to featured component on home teaser (fa413fb)
  • adjusted descriptive teaser text and completed link logic impl (b2a7243)
  • implemented hero banner, home & teaser from projex within platform (41f60b1)

9.36.1 (2023-06-25)

Bug Fixes

  • project pagination with filtering (9d168d5)

9.36.0 (2023-06-24)

Bug Fixes

  • adjusted button behavior (b31f53d)
  • adjusted stylings and add tooltip: (d72a6d4)
  • created download button with anchor-tooltip and removed button el (0fb7dbf)
  • hardcoded theme color values in place of using material getter (e35447e)
  • removed duplicate code in files download button (2a7b73b)
  • removed f-string and console log from carousel constructor (bca4df5)

Features

  • added matToolTip to rerun simulation button (7114b18)

9.35.0 (2023-06-23)

Bug Fixes

  • added attributes to project-chip component (ddb271d)
  • added lintignore as a test (ff08536)
  • added return type on method to appease bots (07a03cb)
  • adjusted files layout (09563a2)
  • adjusted image urls (31093fc)
  • adjusted line height of project files and removed rerun tab (01bd1b0)
  • adjusted profile picture placeholder (47b18dd)
  • adjustments (251f289)
  • increased interactive footprint of project table search chip parent container (9a56611)
  • minor adjustments (4ec806d)
  • removed commented ts code to appease sonarcloud (df9a6b1)
  • removed display from biosimulations notice (7f1dcd0)
  • removed duplicate css code (ab6a18f)
  • removed unsafe sanitizing techniques (74fd796)
  • removed venv dir (ba645b1)

Features

  • added binder notebook linked to interactive notebook test repo (9f51263)

9.34.0 (2023-06-22)

Bug Fixes

  • docs for local docker commands for development (e148835)
  • use nx from repo in CD (9d1adcf)

Features

  • order projects to feature projects which are more highly curated (e85e5b0)

9.33.0 (2023-06-17)

Bug Fixes

  • add test dependency for animation (c77619a)
  • added alt attribute to image tag (33d8fbb)
  • adjusted autoscroll time (f58943e)
  • adjusted colors (979dcde)
  • adjusted header style (2b74b16)
  • adjusted image defaults (5100826)
  • codefactor apply fixes to commit b1d50e9 (32ef241)
  • eslint error about datamodel-database library rootDir (a5c6c4b)
  • linting adjust (8af8e55)
  • minor profile adjustments (eda0a6e)
  • remove default dependency of test phase on build, only combine-api (7fb24c3)
  • removed _blank target from nav button behavior in app hero banner (9a35b52)
  • removed unused undeclared hex colors (57bcb57)

Features

  • added _blank target to project-table selection component (37d167d)
  • added description teaser and verbose description for each featured service in home carousel (0de3775)
  • added image zoom event behavior (8d41722)
  • added images to showcase card (fe2aec1)
  • added learn nav button and tutorials url to config (d708178)
  • added link to rest api in utilities nav button on app banner (4c3db73)
  • added textual heading as placeholder for no profile image (b5ed643)
  • added verbose description on hover for each item in feature showcase (3a24bb3)
  • changes to features hookup (1a13759)
  • implemented href in image placeholder in showcase carousel (115f924)

9.32.0 (2023-06-13)

Bug Fixes

  • adjusted legend (bd34abe)
  • adjusted noPlot template (da31802)
  • adjusted plot legend layout (9e540a3)
  • adjusted plot legend layout (a275988)
  • adjusted plot legend layout and plotparent (38c2ab3)
  • adjusted plotly legend layout and legend (7ba182d)
  • adjustments to browse (3f0f6e0)
  • CodeFactor apply fixes to commit 823d88c (70fe4a8)
  • formatting from CodeFactor (8312259)
  • implemented snack bar for errors (54fd50c)
  • legend adjust (c1638e5)
  • minor adjust (71840e7)
  • moved re-run sim button to top of biocard and implemented snackbar dataclass for customization (3279a7f)
  • overflow adjustment to project scss (11e5397)
  • plot axis names (619d846)
  • standardized/normalized dispatch app nav buttons in hero banner (19f9e1a)

Features

  • added biosimulators button and removed redundant your simulation runs button from dispatch (0664d06)
  • added hover effect to rerun placeholder button (25e7e9f)
  • added rerun simulation button placeholder and snack bar message (c6a4787)
  • added reusable helper methods for axis and legend styling/layout (eea2654)

9.31.0 (2023-06-10)

Bug Fixes

  • added closing div tag to metadata (491d54a)
  • adjusted height of simulation file item expansion panels (386288e)
  • adjusted import ordering to ensure cascading styles (c2de8af)
  • adjusted imports (addc082)
  • adjusted nav button dropdown behavior (9834560)
  • adjusted nav buttons border and css behavior for more reactive design (92b730c)
  • adjustments to appease codefactor (02e853f)
  • disable nx parallel lint build test targets in CI (4a08204)
  • expand single css file budget to 8kb (804cb62)
  • expanded css budgets in projex project.json (b59b4e3)
  • remove .ngcc_lock_file in node_modules and set nx parallel to false (3d5dfdc)
  • removed commented out code and added modifiers (dd0278e)
  • removed commented out code to appease sonarcloud (34e0880)
  • removed dropdown triggerfrom biosimdb and runsim nav buttons (fc51dd5)
  • removed duplicate project details expansion from metadata and migrated into view (18de3e5)
  • removed duplicate spinner container and corresponding ng-container (115aa8a)
  • removed unused css declaration in view component (a762191)
  • synched paginator to data pull (026ae34)

Features

  • added circular border and reactive color scheme to download button in sim profile files tab (e9781a0)
  • added project details to right-col mat-tab-group in simulation page (3a38ec8)
  • added project files expansion (7f13957)
  • added selectable tabs for files and viz (e24b35d)
  • ui: added hovering link color (12cbbb9)

9.30.1 (2023-06-07)

Bug Fixes

  • added -webkit css rules to handle biosimulators button safari glitch (f77e9e9)
  • added event to mat-expansion-panel header for full interactive area (d2a6596)

9.30.0 (2023-06-06)

Bug Fixes

  • added correct routing and behavior to nav buttons (cf7b0a8)
  • added noopener rel in _blank target (d0b00cf)
  • adjusted plot rendering size in simulation profile page (a54363d)
  • adjusted plotparent css class declaration in component html (8a19595)
  • adjusted projects table header name in both platform and projex (d3bbe2a)
  • corrected biosimulators.org routing and corresponding config key name (f218278)
  • removed breadcrumbs from shared navigation component with comment (dcc085d)
  • removed color implementation (7f94a0f)
  • removed commented-out breadcrumb code having it saved locally if we want to re-implement (f0c8125)
  • removed duplicate css class declarations (0ba6e90)

Features

  • added _blank target for biosimulations SOS button (abd457d)
  • added first-page and last-page buttons to Simulation Projects table paginator (a56767c)

9.29.0 (2023-06-04)

Bug Fixes

  • adjusted button behavior (8000f8c)
  • adjusted dropdown menu icon container size (9ff01c9)
  • adjusted nav button behavior to include full-spectrum interactive field (3908d81)
  • adjusted plot iteration rendering (87df355)
  • adjusted plot layout (716b787)
  • adjusted plot rendering size to include axis label (98ac082)
  • adjusted to correct biosimulators.org routing (f20bfee)
  • fixed routing of biosimulators.org button (3c5daba)
  • removed commented out splash page arrow button code in dispatch app (c061d0f)
  • removed link from utils hover-open-menu button (e5cb27d)

Features

  • added _blank target for nav button interaction to open in new tab (9470126)

9.28.1 (2023-06-02)

Bug Fixes

  • path for new summary_filtered and old summary api endpoints (83a6abe)

9.28.0 (2023-06-02)

Bug Fixes

  • adjusted comments in projects table (4d37774)
  • adjusted justification of item alignment in simulation details dropdown (6f2d0ca)
  • adjusted styles (b2a6452)
  • expand single css file budget to 8kb (004570f)
  • formatting fixes from CodeFactor (65308c7)
  • nx build cache output config added to all projects (199dfd3)
  • pagination (ff09ff6)
  • removed hover effect from mat-expansion-panel-header and other headers (47d90fa)

Features

  • serve /projects/summary, /projects/summary_filtered api endpoints (8fb9a4a)

9.27.0 (2023-06-02)

Bug Fixes

Features

  • add projex app to patch project browsing (eaef2e0)

9.26.9 (2023-05-31)

Bug Fixes

  • adjusted fixed position of biosimulators button in app (08e1d1b)
  • point back to production site for all but projects (0629ab3)
  • remove commented code (ffab982)
  • removed second scroll and padding to table and button color (0a41766)

9.26.8 (2023-05-30)

Bug Fixes

  • add citation to project detail summary section (aec51ce)
  • hack to get plots to render on project detail (e34acc8)
  • removed extra import to fix lint error (6ed4f34)

9.26.7 (2023-05-29)

Bug Fixes

  • added correct internal and external routings for features on splash page (2855695)
  • removed commented code for linting (86c3a52)

9.26.6 (2023-05-27)

Bug Fixes

  • display abstract and title even if no thumbnail (bc2b891)
  • project summary partial implementation (2ee990d)
  • respect module boundary, move project-utils to datamodel/common (ff0d73a)
  • updated imports and test cases for project-filter tests (878fe32)

9.26.5 (2023-05-26)

Bug Fixes

  • create-project reactive form fix (2041b04)
  • simulationType checks properly for undefined (1f7ed74)
  • simulator routing fix and linting fix (6e185b8)

9.26.4 (2023-05-25)

Bug Fixes

  • add aria label to simulation summary table per sonar rule (80cbef0)
  • add CNAME for docs.biosimulations.org for docs hosting (863a3fe)
  • increase platform app size budget to 365k/style and 14mb/bundle (3746977)
  • remove unused import in platform app (d234e17)
  • removed biosimulators from featured carousel service (59dc750)
  • simulation page layout and home page footer (211d2e8)
  • unit test needs fake animation (ddf03ec)

9.26.3 (2023-05-23)

Bug Fixes

  • configure docker which is invoked indirectly in builLintTest action (b096643)
  • disable combine-api Docker build cache for failing Github Action (cc67ad8)
  • increase max style size to 115kb on all apps (12c99e0)
  • sonarcloud linting bugs in style sheets (e7c1548)
  • typos for quaternary color, increased style size budget to 115kb (d05b5a2)
  • update docker action versions to fix build error (957c293)
  • upgrade docker github actions and longer timeout on jest test (ce15f6e)

9.26.2 (2023-05-08)

Bug Fixes

  • env NX_SKIP_NX_CACHE in all actions to var NX_SKIP_NX_CACHE_VALUE (b02025e)

9.26.1 (2023-05-08)

Bug Fixes

  • disable nx caching to fix nondeterminism in github actions (a274fce)

9.26.0 (2023-05-07)

Bug Fixes

  • clarify workspace paths for linting and typescript compiler (b4de325)
  • codefactor apply fixes to scss (6a1db66)
  • filter selection compare to break update loop (0cb6355)
  • fix unit test broken by prior sonarcloud fix (62b97d9)
  • lint unused import (68ac7e7)
  • linting errors in account app (bcdd3f0)
  • project table filter works, but component events cycle needs fixing (d6302f5)
  • project table resized to match pagination size without scrolling (03483bf)
  • projects chips and project table test and module imports (9ec2dfa)
  • projects search unit test (7fdfb1d)
  • remove angular material legacy css (abefbbb)
  • remove citations from filter list (30e5ca5)
  • sonarcloud gates for code duplication, sort() and false ip addr (dbf6415)

Features

  • added project filter chips component (f15d5a0)
  • compute server side project filter stats and return to client (c7b5a5e)
  • prototype angular component for project table filtering (15254c6)
  • server side filtering data structures and filter matching function (43ad17f)

9.25.0 (2023-04-24)

Bug Fixes

  • unit test for project-table depends on FormsModule (de1a862)

Features

  • added link from project table to project detail (f8333e3)

9.24.0 (2023-04-23)

Bug Fixes

  • home teaser component CSS partial fix, renders but needs work (63ddd53)
  • nicer layout and styling for new project table (c3572d8)
  • pagination correction in project table (226265f)
  • pagination for project table includes correct number of records (ca1e01b)
  • remove some warnings about CommonJS (e031415)
  • revert prior change regarding CommonJS (ca343f7)
  • template expression linting fix (a365c8c)

Features

  • add server side project pagination and search to api service (a8769ee)
  • connect server side pagination and search to angular client (8c33f6f)
  • responsive project table with search and pagination (50745b7)

9.23.1 (2023-04-17)

Bug Fixes

  • combine-api CORS to allow biosimulations.org/dev (1bd84ce)

9.23.0 (2023-04-17)

Bug Fixes

  • import paths on refactored files (670b353)
  • restore dispatch app / runBioSimulations (effedfe)
  • unit test for user agreement component (f46628b)

Features

  • complete transition of run.biosimulations to biosimulations (c34a933)
  • integrate runBiosimulations (dispatch) & biosimulations (platform) (b500fbf)

9.22.2 (2023-04-12)

Bug Fixes

  • deploy action fails, nx build '--with-deps' flag was removed (7da9f48)

9.22.1 (2023-04-12)

Bug Fixes

  • add openapi-generator to dev deps to run generator locally (6a07747)
  • can't find nx in CI, use npx to invoke (1cfcd10)
  • doc generation to require only Python 3.9 (b361471)
  • install github runner dependencies for format and dependencyLicense (6e70494)
  • install updated node for openapi client gen (1dbcd60)
  • mkdocs action, fix syntax (ed9bb7f)
  • silence some linting rules on generated combine-api angular client (01817e5)
  • update docs path in gen-dependency-license-report (2d8fcd9)
  • update format of some component templates (2bfa620)
  • update node and python in some CI actions (84837f9)
  • update release.yml github action dependencies (d6ce840)

9.21.0 (2022-07-03)

Features

  • add material file input library (f88aa6f)

9.20.1 (2022-06-28)

Bug Fixes

  • dispatch-service: add a queue to the image refresh to handle stale ssh (4e0403d), closes #4304

9.20.0 (2022-06-28)

Bug Fixes

  • platform: fix behavior of back button on featured carousel (4908867)

Features

  • platform: improve appearence of featured cards (a70ca88), closes #4559

9.19.0 (2022-06-27)

Features

  • platform: add a featured projects section to the homepage (867222d), closes #4526

9.18.0 (2022-06-13)

Features

  • add statistics api module (8148a07)
  • api: add ability to get and post statistics (ef50146)
  • platform: add page to view statistics about models (bddd9fd), closes #4527

9.17.2 (2022-06-07)

Bug Fixes

  • api: fix missing acroynm for cellml model language (20ac4ec), closes #4522

9.17.1 (2022-05-29)

Bug Fixes

  • platform: add missing alt tag to image (6f93600)

9.17.0 (2022-05-29)

Features

9.16.0 (2022-05-27)

Bug Fixes

  • platform: applied our color palette to summary charts (ac226d9)
  • platform: correct title of project size chart (5d38879)
  • platform: corrected capitalization of options attribute, cleaned up colors of line charts (52abebd)

Features

  • platform: added alternatiing background to summary sections and fixed width (53b1fe7)
  • platform: cleaned up arrangement of summary plots and titles (be6de1d)
  • platform: hid chart titles which are redundant with section headings (700a13b)
  • platform: reordered summary sections and cleaned up titles and variable names (68c3c02)

9.15.1 (2022-05-26)

Bug Fixes

  • platform: remove incorrect home section, add back about section (3cc4758)

9.15.0 (2022-05-26)

Features

  • platform: add a statistics view page (e019b6c)

9.14.1 (2022-05-15)

Bug Fixes

  • dispatch: fix data generator id set during archive creation (12c4526)

9.14.0 (2022-05-09)

Bug Fixes

  • dispatch: fix type Chooose -> Choose (226b5ff)

Features

  • dispatch: apply a new design to the dispatch component (905e545)
  • dispatch: apply new style to the create project form (b6ef601)

9.13.6 (2022-04-11)

Bug Fixes

  • separated URIs for SVG and SVGZ (13bf805)

9.13.5 (2022-04-08)

Performance Improvements

  • dispatch-service: increase the number of retries for uploading results to hsds (fc80ba4)

9.13.4 (2022-03-30)

Bug Fixes

  • combine-api: add protocol to biotext url for cors (5e7c9e0)

9.13.3 (2022-03-26)

Bug Fixes

  • combine-api: add libretext to cors (adfdd37)
  • dispatch: ensure params can be fetched for models provided by url (a708c1b)

9.13.2 (2022-03-02)

Bug Fixes

  • fixed URI for dc namespace, enabled SBML draft packages (b3ec967)

9.13.1 (2022-02-28)

Performance Improvements

  • combine-api: sped up getting specifications of available simulation tools (044bd80)

9.13.0 (2022-02-28)

Features

  • combine-api: improved timeout error messages (12f02e4)

Performance Improvements

  • combine-api: tweaked settings to improve simulation execution (45517ae)

9.12.1 (2022-02-28)

Bug Fixes

  • dispatch-service: increased reliability of retrieving logs from S3 (4c036ac)

9.12.0 (2022-02-28)

Features

  • combine-api: updated to BioNetGen 2.8.0 (73e6589)
  • combine-api: updated to biosimulators-utils 0.1.66, biosimulators-xpp 0.0.12 (3fe0ad4)

9.11.3 (2022-02-27)

Bug Fixes

  • dispatch-service: restored retrying for image refreshing (ca2d8be)

9.11.2 (2022-02-26)

Bug Fixes

  • dispatch-service: fixed extraction of larger COMBINE archives (6274023)
  • dispatch,platform: fixed size of images in markdown descriptions of projects (df64f0c)

Reverts

  • dispatch-service: reverted to reading manifests out of COMBINE archives (c2dc2ab)

9.11.1 (2022-02-26)

Bug Fixes

  • dispatch-service: fixed saving thumbnails in subdirectories of COMBINE archives (01cff26)

9.11.0 (2022-02-25)

Bug Fixes

  • dispatch-service: fixed formatting of post-processing error messages (9fe1030)

Features

  • combine-api: updated BioSimulators-utils to 0.1.163 and updated simulation tools (bef3660)

Reverts

  • combine-api: reverted to BioNetGen 2.7.0 (66a255c)

9.10.0 (2022-02-23)

Features

  • combine-api: updated to biosimulators-utils 0.1.162 (58ab3a3)
  • dispatch: soften language about warnings in simulation projects (38d4476)

9.9.1 (2022-02-23)

Bug Fixes

  • platform: fixed simulation type labels in project browse controls (694cb6f)

9.9.0 (2022-02-23)

Features

  • dispatch-service: organized Slurm scripts and logs for refreshing images (8248642)

9.8.1 (2022-02-23)

Bug Fixes

  • api: fixed path to output archives (155076b)
  • dispatch-service: corrected error tracking of S3 uploads, always trying to upload results to S3 (ab40b15)
  • dispatch-service: fix temporary directories for containers (190824c)

9.8.0 (2022-02-22)

Bug Fixes

  • combine-api: fixed JSON serialization for Swagger app (6d59f90)
  • combine-api: fixed JSON serialization for Swagger app by replacing ujson with orjson (e10c291)

Features

  • combine-api: upgraded Brian2, pyNeuroML, NEURON (329e07a)

Performance Improvements

  • combine-api: decreasing number of requests in between restarting (438c6fb)

9.7.4 (2022-02-19)

Performance Improvements

  • combine-api: sped up JSON encoding (44fe6c1)

9.7.3 (2022-02-19)

Bug Fixes

  • dispatch-service: corrected capitalization of SED-ML, COMBINE (e267376)

Performance Improvements

  • combine-api: added ability to directly parse OMEX manifest files (a43a50e)
  • dispatch-service: switched to directly parsing manifests (b86f48c)

9.7.2 (2022-02-19)

Bug Fixes

  • api: handled older simulation specifications that lack styles (01d7829)

9.7.1 (2022-02-18)

Bug Fixes

  • api: set minimum file size to 0 (6daf637)
  • dispatch,platform: fixed default plot stroke width (637a59c)

9.7.0 (2022-02-18)

Features

  • dispatch,platform: disabled 2d plots for 1d data (3dcbe8a)

9.6.4 (2022-02-18)

Performance Improvements

  • dispatch-service: clear out the old jobs from queue immediately after completion (3732d84), closes #4236

9.6.3 (2022-02-17)

Bug Fixes

9.6.2 (2022-02-17)

Performance Improvements

  • dispatch-service: tweak stall settings for cpu intensive jobs (b3e651c)

9.6.1 (2022-02-16)

Bug Fixes

  • dispatch,platform: align rendering of styles with SED-ML L1V4 (8e9b50d)

9.6.0 (2022-02-15)

Features

  • combine-api,api,dispatch,platform: added support for SED-ML L1V4 styles (1144336)

9.5.2 (2022-02-14)

Bug Fixes

  • dispatch: restore /simulations links (e86f8f6)

9.5.1 (2022-02-14)

Performance Improvements

  • api,dispatch-service: move downloading COMBINE archive and uploading to S3 to dispatch service (c325b7b)

9.5.0 (2022-02-13)

Features

  • combine-api: upgraded to flask 2, connexion 2.11, openapi-schema-validator 0.2 (9242e7d)

9.4.0 (2022-02-13)

Features

  • combine-api: added endpoint for modifying COMBINE/OMEX archives (01acfaa)

9.3.0 (2022-02-12)

Bug Fixes

  • platform: displayed model formats for projects; closes #4098 (624b03c)

Features

9.2.4 (2022-02-12)

Bug Fixes

  • platform: truncated JSON-LD descriptions (5fbb023)

9.2.3 (2022-02-11)

Bug Fixes

  • dispatch-service: remove http retries on combine wrapper service (8239f3d), closes #4032

9.2.2 (2022-02-08)

Bug Fixes

  • dispatch: make type of citation in JSON-LD data compatible with Google (fa1b5b3)
  • platform,dispatch: modify citation in schema.org metadata for compatibility with Google (0f2bfc3), closes #4179

9.2.1 (2022-02-08)

Bug Fixes

9.2.0 (2022-02-07)

Features

  • add shared rxjs-backoff library (e27269e)

9.1.2 (2022-02-07)

Bug Fixes

  • fix height for consent screen on mobile (30efa91), closes #4143

9.1.1 (2022-02-07)

Bug Fixes

  • dispatch-service: bind the /tmp directory to /local on HPC (3d05da1), closes #4135

9.1.0 (2022-02-07)

Features

  • add version to environment (0bca178)

9.0.5 (2022-02-07)

Bug Fixes

  • api,dispatch-service: remove completed and failed jobs from queue (bbf3301), closes #4176
  • dispatch-service: correct ordering of processing steps in job, clean up log (61115d2), closes #4113

9.0.4 (2022-02-06)

Bug Fixes

  • platform: fix display of thumnails in browse (34cc39f)

9.0.3 (2022-02-05)

Bug Fixes

  • use custom version of nestjs/bullmq (9161dbd)

9.0.2 (2022-02-05)

Bug Fixes

9.0.1 (2022-02-04)

Bug Fixes

  • api: fix health indicator queue connection (d39463e)
  • deps: update nrwl and angular (f6188be)
  • dispatch-service: fix flow processor connection options to queue (0150b1e)
  • dispatch-service: fix queue connection for dashboard (3971d9f)
  • fix connection options for queues (26a67f2)

9.0.0 (2022-02-03)

Bug Fixes

  • api: fix bull health check (d953e60)
  • api: handle case when metadata is missing (48dd040)
  • api: handle case when thumnails urls are not defined (e0e7816)
  • api: prevent process crash for missing results and improve error handling (50f62ff), closes #4007
  • combine-api: fixed configuration of Gunicorn deployment (9acd09f)
  • combine-api: reset timeout to 30 s (ee162ee)
  • config: fixed value of platformApp in endpointsTemplate (61d2d5f)
  • dispatch-service: add retrying for job submission to hpc (8161089), closes #4099
  • dispatch-service: fix ssh connection for stale connections (ef44d57), closes #4099
  • dispatch-service: handle dependency between archive extraction and thumbnail generation (9f94cee), closes #4063
  • dispatch-service: modify sbatch script to get correct content tyes (85259ab), closes #4106
  • ui: fixed updating of table (43d87b9)
  • update angular and nrwl dependencies (f5edd62)

Code Refactoring

  • api: remove statusReason field from SimulationRun (3c2e670), closes #4111

Features

  • add cors and lifecycle config for storage buckets (fe3e622), closes #3994
  • api,simulators-api: support additional variants of true for query arguments (116d6c2)
  • api: add endpoint for putting endpoints of files. (6aecd5b)
  • api: add endpoint to download files and thumbnails (2b41eba), closes #3981
  • api: standardized error messages (3264f1e)
  • api: standardized titles of errors (92c2e0b)
  • combine-api: update to BioNetGen 2.7.0 (f2b53a1)
  • combine-api: updated dependencies (9f0e1a2)
  • combine-api: updated to assimulo 3.2.9 (f323461)
  • combine-api: updated to biosimulators-utils 0.1.157 (0df1218)
  • combine-api: updated to biosimulators-utils 0.1.159 (469461e)
  • dispatch-service: add final processing step for simulation runs (d994867)
  • dispatch-service: add processors for each step of simulation run workflow (79aaa35)
  • dispatch-service: add retries to ssh commands that fail to submit (f7d6a05)
  • dispatch-service: add ui to monitor queues (a9fc321)
  • dispatch-service: define queues and jobs for simulation workflow (cb4fac1)
  • dispatch-service: improve logging of post-processing steps failures (a09c4c4)
  • dispatch,platform,ui: added ability to render URIs such as for emails and telephones (83a7f56)
  • ontology: added formats used with ModelDB (da23b89)
  • relaxed license requirement for projects (87cf473)
  • storage: add datamodel and methods for getting output files (9cd4b19)
  • update maximum upload sizes and documentation (14b0b5d)

Performance Improvements

  • api,dispatch-service: change storage backend to Google Cloud (9c26643), closes #4039
  • api,dispatch-service: update from Bull to BullMQ (21717ff)
  • api: improve specs and files reliability (b335f4b)
  • combine-api: improve production runner for combine-api (c50c48b)
  • combine-api: tweak deployment settings (84693eb)
  • dispatch-service: increase concurrency for monitoring jobs (2865213)
  • dispatch-service: increase concurrency of proccessing steps (0a8f769), closes #4047
  • dispatch-service: increase processor concurrency to 10 (388154d)
  • dispatch-service: maintain persistent ssh connections (acccba7)
  • dispatch-service: update archiver servcie to use s3 instead of ssh (214918d)
  • dispatch-service: use s3 to get logs, simplify workflow (8fafd09)
  • storage: switched to streaming downloaded files to S3 (8caed80)

Reverts

  • "[CodeFactor] Apply fixes to commit ede3534" (234107f)
  • "refactor(dispatch-service): moved hsload to complete processor" (13f9f82)
  • "refactor(dispatch-service): moved archive uploading to dispatch processor" (5db7ea1)
  • revert "chore: format files. [skip ci]" (d9457ca)

BREAKING CHANGES

  • api: the statusReason field has been removed from the api response

8.8.0 (2022-01-08)

Features

  • added workflow to delete temporary COMBINE archives (0d722e9)
  • api,combine-api,dispatch,platform: added support for references for projects (a544969)

8.7.1 (2022-01-06)

Bug Fixes

  • add script ignore false to sharp install (9b90d9b)
  • dispatch-service: added dependency for sharp to Dockerfile (ba344c7)
  • dispatch,platform: fixed name and URL for log format in files tab (f13647f)

8.7.0 (2022-01-06)

Bug Fixes

  • dispatch-service: separated input and output files for simulation runs (dc98a46)
  • dispatch,platform,ui: corrected layout of metadata columns (8044bc6)
  • dispatch,platform: added modeling methods to metadata (6da720e)
  • dispatch: add rel noopenor for external links (9efa059)
  • ui: fixed setting of open control panel in table controls (ca529a3)

Features

  • combine-api: added utility methods for reading S3 files (4e3df4f)
  • dispatch-service: added support for SLURM constraints (df2acba)
  • dispatch,platform,ui: added markdown rendering for project descriptions (818d267)
  • dispatch,platform,ui: interleaved metadata about files into files tab (9807406)
  • dispatch: made it easier to get errors with simulation projects (4c7635f)
  • ontology: added additional formats used by Physiome (3e951d0)

Performance Improvements

  • api: added caching for getting properties of ontology terms (c273e88)
  • dispatch,platform: reduced thumbnail image sizes (049af36)

8.6.0 (2021-12-31)

Features

  • ontology: added formats used by Physiome model repository (b407218)

8.5.6 (2021-12-27)

Bug Fixes

  • update package lock version (b91c669)

8.5.5 (2021-12-23)

Bug Fixes

  • api: tried to correct logging for errors in uploading archives (b492f02)

8.5.4 (2021-12-23)

Bug Fixes

  • improved error logging, increasing AWS timeout (cccf802)

8.5.3 (2021-12-23)

Bug Fixes

  • dispatch-service: fixed retrying of files and specs to avoid conflicts on incomplete posts (620f0eb)

8.5.2 (2021-12-23)

Bug Fixes

  • api,dispatch-service: fixed logging for complete processor failures (f2119d4)

8.5.1 (2021-12-23)

Bug Fixes

  • dispatch-service: retry project publication after run completion (e686664)

8.5.0 (2021-12-22)

Bug Fixes

  • simulators-api: fixed updating of updated timestamp; addresses #3878 (13ee425)
  • ui,dispatch: fixed unselecting files; closes #3875 (2f84e18)

Features

  • ui: added instructions to refresh on failures (0181c3b)

8.4.1 (2021-12-22)

Bug Fixes

  • combine-api: fixed reading shared configuration (5a83e6e)

8.4.0 (2021-12-22)

Bug Fixes

  • added project id, owner to CompleteJob for failures (0a8d834)
  • api,dispatch: fixed data model for simulation results (7cd2b5e)
  • api,dispatch: fixed data type for simulation results (610cbc9)
  • api: changed file URL validation to allow un-encoded URLs (f78bc43)
  • fixed external simulators API endpoint (25b3a3c)
  • fixed spinner for loading table data (e2e1314)

Features

  • added checks that S3 files were deleted (390300c)
  • api: added cache for project summaries (6fc5bb7)
  • api: added checks that S3 files were deleted (5d3ccb9)
  • api: added handled for NaN and Inf from HSDS (7802310)
  • combine-api: relaxed required metadata for simulation projects (2be28f1)
  • directed href targets (d609f80)

8.3.0 (2021-12-20)

Bug Fixes

  • dispatch-service: fix dispatch service post limit (95653f8), closes #3828
  • dispatch: correct security issue with untrusted html input (8b464b6)
  • ui: fixed spinner exit for table component (f26802c)

Features

  • api: added project summary caching at creation and updating (20d99f2)
  • dispatch: added example simulation runs for Brian 2 (710df68)

8.2.1 (2021-12-16)

Bug Fixes

  • add gtag snippet to dispatch and simulators (f1b6332)
  • config: add default server limit to config (496b430), closes #3828

8.2.0 (2021-12-16)

Bug Fixes

Features

  • add angular analytics package (3363f7b)
  • added implementation of analytics and user consent (2d87bb1)
  • dispatch,platform,simulators: add cookie consent and privacy settings to frontend apps (e84cdea)

8.1.0 (2021-12-16)

Bug Fixes

  • fixed display of files in subdirectories (ee62bbe)
  • fixed file size extraction for empty files (b3dce39)
  • fixed simulators view endpoint method (e40f4cd)
  • set minimum time step to 1 (e92ffa5)

Features

  • combine-api: added error messages for invalid S3 bucket configuration (626a2f2)

8.0.0 (2021-12-15)

Bug Fixes

  • config: change name of env variable to avoid clash (caf69f4)
  • config: correct endpoints for s3 contents path. Add some testing (73f6034), closes #3755
  • config: fix endpoints for ontology url (f7ba9c5), closes #3771
  • config: fix prod file url (5211afd)
  • config: fix storage health endpoint (14d303c)
  • dispatch-service: corrected storage endpoint in sbatch sevice to external (8eb34d4)
  • fixed broken links in documentation (fe96ded)
  • fixed broken links in documentation (8de8a6f)
  • removed invalid and unecessary workflow_call secret inputs (b925dfe)
  • simulators-api: fix permissions for deletion of all simulation runs (24aef29), closes #3767

Code Refactoring

  • api: simplify management of files (e16c35f)

Features

  • api,dispatch-service,dispatch: expanded to full SED-ML data model (2550def)
  • api: improved error logging (4d75193)
  • auth: add scope for deleting all simulation runs (77a859c)
  • combine-api: expanded to full Python SED-ML data model (912f8d5)
  • combine-api: updated dependencies (a7bf6e9)
  • config: load endpoints dynamically if not in browser (90ddc18), closes #3585
  • dispatch-service: added env variables to enable simulators to get number of CPUs (fbdf8fa)
  • dispatch,dispatch-service: added support for multidimensional plots (6681d25)
  • dispatch,platform,api: added filter and display of SED-ML file provenance (d2a6c29)
  • dispatch: extend vega export to multidimensional data (4474f0c)
  • expanded COMBINE archive creation to all types of model changes (f65ffc5)

Performance Improvements

  • api: extract the combine archive directly on s3 via streams (b5a0f08), closes #3094

Reverts

  • "chore(deps): update dependency typescript to v4.5.4" (f40932e)
  • "chore(deps): update typescript-eslint monorepo to v5.7.0" (dee846f)
  • "chore(deps): update typescript-eslint monorepo to v5.7.0" (16bcd80)

BREAKING CHANGES

  • api: the download project endpoint will fail for all previously submitted simulation runs. Runs submitted prior to this change will not be retrievable by the api or applications

7.0.0 (2021-12-02)

Bug Fixes

  • api,dispatch-service,hsds: fixed retrying in APIs (b3109a1)
  • config: reverted changes to localhost (04f2c42)
  • corrected BioSimulators auth audience (5c8b18d)
  • corrected BioSimulators auth audience (fce4347)
  • corrected filtering for numerical columns (d4bf35f)
  • dispatch: fix displaying of data in cases where simulation fails and metadata is not present (da18704), closes #3705
  • dispatch: fix file uploading (30f9cb9), closes #3719
  • dispatch: fix uploading of files (f597e90), closes #3719
  • fixed validation by upgrading from broken version of class-transformer (ca20307)
  • platform,ui: fixed project browse for mobile (fcfb552)
  • platform: fixed position of seach/filter button (133f08c)
  • ui: fixed autocomplete filter (cb26564)

Features

  • added ability to filter and search projects (21c14b4)
  • added new component to enable components for routes to push buttons into the breadcrumbs area (7918db1)
  • api,dispatch,dispatch-service: expanded support for failed simulation runs (9e7e71c)
  • api,platform: added owners, organizations to project view with hyperlinks (63d9457)
  • api,platform: started to display ownership of projects (6f8378a)
  • api: add check for data service to status check (d8fbbc5), closes #3649
  • api: added new scope for externally validating simulation runs (e3bd698)
  • api: added URLs to accounts, organizations (c6926b9)
  • api: began to limit publication requests to model repositories (e830002)
  • api: working on restricting requests for publication with simulation run requests (af7b6a0)
  • dispatch: clarified units of columns of simulation runs table (3ae498e)
  • improved table searching for data with accents (d33617b)
  • platform: added filter for publication status (509eaa4)
  • platform: scroll to top on opening projects search/filter (26de2b6)
  • platform: started to add filtering and searching for projects (2505d7f)
  • simulators: expanded simulators filters (1a76b7e)
  • ui,platform: added autocomplete filter for attributes with many values (049869f)
  • ui: add custom caruousel component (9a61d4f)
  • ui: replace npn-slider with custom component (1cc79d5), closes #3706

Performance Improvements

  • api,dispatch,dispatch-service,simulators-api: removed unnecessary return of new resources (5fce07f)
  • api: don't return the log after creating (5e37c6e), closes #3609

Reverts

  • Revert "refactor(auth): removed auth/open endpoint" (f983628)
  • "refactor: cleaned up building Angular apps" (d21b2ed)
  • revert "refactor: organized endpoints configuration" (a5e93c3), closes #3625
  • revert change to build front end apps (5870fbf)

BREAKING CHANGES

  • api: The logs post endpoint no longer returns the log that was created. For that, use a GET request after posting the log.

6.1.0 (2021-11-14)

Bug Fixes

  • auth: fix import (a7ba6b8)
  • auth: handle case of no custom permissions (1c3d760)
  • corrected capitalization of BioSimulations (3d981ee)
  • debugged testing COMBINE API (35672ce)
  • debugged testing COMBINE API (d18cb86)
  • debugged testing COMBINE API (2a1e6b3)
  • debugged testing COMBINE API (c7e1cb9)
  • dispatch: corrected run URLs in check simulation run tool (a1894fa)
  • dispatch: fixed dispatch simulation run view; closes #3088 (26a8d5a)
  • dispatch: fixed highlight.js import for log formatting (0320cc2)
  • fixed links, warnings (ecb68fe)
  • fixed python code highlighting (ef88e12)
  • fixed typos, added spelling exceptions (7c77dc2)
  • removed example with COMBINE archive that intentionally fails (04b4c6e)

Features

  • api,dispatch-service: improved error messages and retrying (a6b2693)
  • api: improved reporting of errors with inconsistent data (1c6c223)
  • dispatch-service: add logging to processing posts to api (1ca1900)
  • dispatch-service: add retries for posting processing results (fe9cddc), closes #3531
  • improved docs (ab6722b)
  • improved docs (209a421)

6.0.2 (2021-11-10)

Bug Fixes

6.0.1 (2021-11-10)

Bug Fixes

  • api: fixed IsImageDigest validator for non-strings (53501b1)

6.0.0 (2021-11-04)

Bug Fixes

  • api: build fix for new axios types (e7ea984)
  • dispatch-service: add a temporary check for mistructured logs (a67bfa1), closes #3482 #3482
  • dispatch-service: remove ssl skip when downloading archive (b4bd2c0), closes #3092
  • dispatch,api,dispatch-service: fixed data model for exceptions in simulation run logs (191f1d3)
  • fix imports (a076005)
  • simulators: fixed text overflow of simulator test results (7a8b11a)

Code Refactoring

  • api: cleaned up simulation run files (0213fb5)

Features

  • added endpoints for getting summaries of projects (2e9a54e)
  • api: added database model and validation for logs (6a3a344)
  • api: added endpoints for getting individual SED elements; closes #3439 (8aa64fc)
  • combine-api: add dynamic module for combine api-client (e7c2448), closes #3180
  • datamodel: add validation for image digests (6106e54)
  • dispatch-service: enhanced tracking of processing results (b4f01e3)
  • dispatch: updated publication form, finished switching to Endpoints (a5bef72)
  • exceptions: improve error handling (4a3e8c7)
  • hsds: handle transient hsds query failures (f4a19f5), closes #3413
  • ontology: added parent/child relationships to ontology terms (4107f1d)
  • simulators-api: add validation for api models (ce2c5bb)
  • simulators,dispatch,platform: added status bar to bottom of apps; closes #3210 (3630c23)

Reverts

  • dispatch-service: revert using new config service to provide basepath (e479d2e)

BREAKING CHANGES

  • api: moves simulation run file information from 'Simulation Files' collection

5.9.0 (2021-10-24)

Bug Fixes

Features

  • api: add caching to results and ontology endpoints (bb2a991)
  • api: add caching to results endpoints (ed54363)
  • api: add health check for job queue (a05556e)
  • api: add health module and endpoints (da036f5)
  • api: add various health checks and endpoints (d30c7d2)
  • api: setup results cache with REDIS (3e40fde)
  • dispatch-service: add limit for retries of status for jobs (f187b03)
  • dispatch,platform: added structured data for projects, simulation runs: (7135ed0)
  • dispatch,simulators: added structured data tutorials (5c23e8d)
  • dispatch,simulators: encoded FAQs into Schema.org (936fb44)
  • exceptions: dont process health check http exceptions (b75747e)
  • simulators-api,api: added clearer payload too large messages (98fb49d)
  • simulators-api: add health checks for simulators-api (26d3b63)
  • simulators: added structured data for simulators as software applications (7618db3)

Reverts

  • simulators-api,api: revert partially the changes in 98fb49d651c01d621d175051cb030621b273034a (d88fcea)

5.8.0 (2021-10-20)

Features

  • api: enabling simulation run requests with latest version of a simulator (2b7c2d9)
  • config: added endpoint for latest versions of simulators (2a582ee)
  • dispatch: recorded simulator versions and digests for simulation runs (f2abb39)
  • simulators: added validation that version isn't reserved word 'latest' (47843a8)

5.7.3 (2021-10-19)

Bug Fixes

  • api: correct field name to get values from dataservice (53a6bbc), closes #3313
  • api: fix typo with checks (caada0a)

5.7.2 (2021-10-19)

Bug Fixes

  • api: aligned parameter name in documentation (0100a27)
  • simulators-api: corrected put method; closes #3305 (57c34be)

5.7.1 (2021-10-18)

Bug Fixes

  • account-api: fixed route parameter names (c7d8712)
  • api: fixed route parameter names (1496f0f)

5.7.0 (2021-10-18)

Bug Fixes

  • api: fix docs and typing of open api definition (#3307) (0640c6a), closes #3304
  • api: fix param name parsing for projectId (af3c406)
  • combine-service: added missing Swagger templates to Docker image (f27b8c8)

Features

  • combine-service: added health endpoint (0d356d3)
  • combine-service: increased file upload limit, clarified error message (5dfa25c)

5.6.2 (2021-10-18)

Bug Fixes

  • api: fix module import (d47c376)
  • dispatch: corrected file types for validate OMEX metadata form (98794cd)

5.6.1 (2021-10-18)

Bug Fixes

  • api: fix permissions for endpoints (f00f6d1), closes #3242
  • update client ids for api docs (1ec36bb)

5.6.0 (2021-10-17)

Bug Fixes

  • api: update api to use updated hsds client (e7832aa)
  • dispatch: add flag to skip downloading test results to simulators service (cbd63cc), closes #3197
  • dispatch: fix alg list to empty list to prevent crashing (338be99)
  • make changes to update mongoose (4653155)
  • platform,dispatch: corrected link to simulation results in files tab (00aa363)
  • platform: redirect to 404 for non-existent projects; closes #3234 (173439a)
  • simulators: fix json-ld metadata on index.html (95b3d98)

Features

  • api: add custom styling to swagger ui (90830c0)
  • hsds: update client library (5746832)
  • simulators: added repository digest to image model; closes #3194 (1293410)
  • simulators: expanded full text search; closes #3209 (c877189)

Reverts

  • deps: revert update dependency eslint to v8 (0fdb3d8)

5.5.0 (2021-10-09)

Bug Fixes

  • simulators-api: add biosimulations.org to cors (c2eea89)

Features

  • api: add case-insenstive unique index for project ids (5f96f91), closes #3160
  • api: add controller level validation for project ids (cdba9ce)
  • dispatch: added check that simulation run was successful (b4ade32)
  • platform: added validation for project ids; closes #3183 (01b6178)

5.4.0 (2021-10-08)

Bug Fixes

  • combine-service: update combine-service client to latest api changes (74a70d8)
  • dispatch,platform: fixed visualization rendering when groups of datasets are selected (f205ab4)
  • dispatch: handle cases when metadata is empty without throwing error (57a16c5)

Features

  • combine-service: added endpoints for validation (f602e65)
  • combine-service: updated to biosimulators-utils 0.1.130 (e46d13e)
  • dispatch: add some error handling (6cc7f62), closes #3088
  • dispatch: added forms for validating models, simulations and metadata (d7991ed)
  • dispatch: added options to project validation (eebd16f)

Reverts

  • combine-service: reverted URL for COMBINE API (d1dd8b5)

5.3.0 (2021-10-07)

Bug Fixes

  • added 'master' attribute to file object (5f4f722)
  • api,mail-service: update api client to return observable (d26ce89), closes #3102
  • api: add permissions to get all specs (dbce421), closes #3136
  • deps: update dependency rxjs to v7.3.1 (8cb2d32)
  • deps: update nest (f7a97e6)
  • dispatch: fixed lint issue (660bcb8)
  • fixed lint issue (e82e6fc)
  • platform,dispatch: fixed plotly tests (f2d8353)
  • simulators-api: allow cors for biosimulatiors.dev (1d93452)
  • ui: fixed display of errors with Vega visualizations (1270955)
  • ui: fixed Vega export for 1-d heatmaps (cd5713d)

Features

  • api: create project endpoints (d1b9fe7), closes #3067
  • combine-service: added options for validation of COMBINE archives (42febbe)
  • combine-service: added options to control COMBINE archive validation (b4c0c12)
  • combine-service: added timeout for simulation execution (8eb8deb)
  • combine-service: update combine-api client (77c2f6d)
  • datamodel: add project datamodel (57cf45c)
  • dispatch,platform,simulators: improve recognition of Vega files by media type (5f0051b)
  • dispatch: added options for validating COMBINE archives (7d0a815)
  • platform: added export of visualizations to Vega and COMBINE archives (fce6731)
  • platform: added heatmap, line plots (84898db)
  • platform: added histogram visualization (7a6abfa)
  • platform: added SED-ML visualizations (2ac40b3)
  • platform: added simulation types and algorithms to simulaton overview (4c768e5)
  • platform: added vega export for heatmaps and line plots (a8c9ad4)
  • platform: front end displays projects from api (9ecfa80), closes #3149
  • ui: added ability to attach hyperlinks to menu items (7ca3d10)

Reverts

  • deps: revert 235c9db3e9649cdb8b42e6575517aa651f9e1c2d (05cb6f3)

5.2.0 (2021-10-04)

Bug Fixes

  • api: add authentication to post metadata (999e2b9), closes #2865
  • deps: update dependency @sendgrid/mail to v7.4.7 (bae8e96)
  • dispatch-service: fix processing of environment variables (cb0aa04)
  • dispatch-service: process metadata with other processing (7f8f44a), closes #3046

Features

  • api: add endpoints to get particular specifications for simulation runs (87eede1)
  • api: add file object (39f25f3), closes #2914
  • api: create specifications object and endpoints (aca4786)
  • dispatch-service: process files and sedml specs (fb37624)
  • dispatch-service: send sedml specifications to the api (7d6a8c7)

5.1.1 (2021-10-01)

Bug Fixes

  • platform: corrected handling of software license keys for simulation (84bef20)
  • platform: corrected handling of software license keys for simulation (aba13fe)

5.1.0 (2021-09-29)

Bug Fixes

  • deps: update dependency auth0 to v2.36.2 (#3076) [skip ci] (a696fbc)
  • dispatch-api: fix cors for biosimulators (22439d2)

Features

  • dispatch: require configuration of academic use for commercial solvers (6c5307c)

5.0.0 (2021-09-28)

Bug Fixes

  • dispatch-service: fix type error when processing metadata (a646c98)
  • make datamodel consistent for license (4b95e4d), closes #3050
  • dispatch-api: remove extra slash for metadata uris (b627e74), closes #3052
  • ensure external url is used for combine api (2d98aba)
  • dispatch: corrected when metadata about simulation projects is retrieved (1682d83)

Code Refactoring

Features

  • dispatch-api: ensure only public models are shown for platform (#3045) (5619c03), closes #3044
  • dispatch-api: extract files to s3 and replace combine archive file extraction endpoint (56f8413), closes #2945
  • dispatch-api: upload omex files to s3 from url (4d8f780)

Reverts

  • dispatch-api: revert permissions change in 3175c6378160f34e8389b6e501ea2534eb9d4c12 (5ab7d08)

BREAKING CHANGES

  • The ontology, dispatch, and platform apis are consolidated into one main backend api for biosimulations. There is a seperate api for biosimulators. The combine-service also provides a rest api that is mostly intended for internal use.

4.6.0 (2021-09-27)

Bug Fixes

  • deps: update dependency aws-sdk to v2.995.0 (19b509a)
  • dispatch: improved handling of undefined simulations in simulations browse view; closes #2999 (bf47994)
  • platform: handle cases when metadata is missing (f738a74)

Features

  • simulators: improved specification of simulator CLIs; closes #3015 (c396bfa)
  • create alternate vega view component (453a109)
  • dispatch: added license confirmation to publish run form (1889e1e)
  • dispatch,platform: updated terms about granting BioSimulations to distribute projects (6ee2bb1)
  • platform: add code to get metadata and specs of visualiazations (0cdc472)
  • platform: add support for showing vega figures (f011480)
  • ui: allow for conditional loading of tabs (1b4779f)
  • updated biosimulators-utils, biosimulators-bionetgen (ce75ea6)

Performance Improvements

4.5.0 (2021-09-26)

Features

  • simulators: improved simulator usage examples; closes #3016 (a56dea2)

4.4.2 (2021-09-23)

Bug Fixes

  • simulators-api: fixed sorting of simulator versions with > 4 points (020073a), closes #3008

Reverts

4.4.1 (2021-09-22)

Bug Fixes

  • fixed sorting of simulator versions with > 4 points (e0b60ce)

4.4.0 (2021-09-22)

Features

  • ontology: updated to KiSAO 2.29 (31e7d7b)
  • platform: improve styling of platform browse (28e8e1d)

Reverts

  • remove ui commit scope [skip ci] (5051250)

4.3.0 (2021-09-15)

Bug Fixes

  • deps: update dependency @stoplight/json-ref-resolver to v3.1.3 (#2986) (fe9c5f3)
  • deps: update dependency bull to v3.29.2 (#2987) (98cbebf)
  • dispatch: proceed if metadata is missing (#2998) (f09c633), closes #2994

Features

  • simulators: expanded specs for simulators (32b100b)
  • expanded simulator specs (f281cd3)

4.2.0 (2021-09-11)

Bug Fixes

  • deps: update dependency axios to v0.21.4 (#2952) (c24c0e2)
  • deps: update dependency ssh2 to v1.4.0 (#2953) (a3afb2b)
  • specify global setTimeout instead of window (432b90a)
  • dispatch-service: restore check for empty env variables (3f714ba)
  • restore mkdocs file location (41a269e)

Features

  • account-api: replace typegoose with mongoose (69911a3)
  • dispatch-api: handle errors and timeouts on uploa> (dad35ea), closes #2860
  • dispatch-service: added passing software licenses from deployment secrets to Singularity run (cc19999)
  • storage: add simulation storage service and timeout for s3 uploads (0c24173)

4.1.0 (2021-09-06)

Features

  • simulators: added attribute to track installation instructions for Python APIs (cb2b415)

4.0.1 (2021-09-06)

Bug Fixes

  • dispatch: simulation results URLs for data visualizations (9b7b879)

Reverts

  • 39a60b17d640b62639f6594024f4ba4c66baedc5 (f804cce), closes #2959

4.0.0 (2021-09-04)

Bug Fixes

  • dispatch: properly encode uri to allow for fetching results (dcbf044)

Features

BREAKING CHANGES

  • simulation runs sumbitted prior to the update will not display on the dispatch app

3.20.0 (2021-09-04)

Bug Fixes

  • deps: update dependency aws-sdk to v2.983.0 (#2947) (39a60b1)
  • dispatch-service: correct the determination of the environment (ce46d3b)
  • fix default environment to dev (c970ccd)
  • new endpoint implementation (ed42b6b), closes #2943 #2861 #2859

Features

  • dispatch,dispatch-api: move thumbnail processing to backend (4495d6d)
  • platform: add page to view projects on platform (e568d0c)

Reverts

  • revert commit 5dad745d1df0ffc3fb2fba8fc3b99b21b69b0521 (f8cdd5b)

3.19.0 (2021-09-02)

Features

  • combine-service: updated to biosimulators-utils 0.1.115, biosimulators-amici 0.1.18 (9ad2945)

3.18.0 (2021-09-01)

Bug Fixes

Features

  • combine-service: fixed error handling for run sim, simplified run sim options (5e63d49)
  • dispatch: added support for new SBO modeling framework terms (80ee759)

3.17.0 (2021-09-01)

Bug Fixes

  • deps: update dependency aws-sdk to v2.980.0 (#2906) (163191d)

Features

  • add shared config file support (976e578)
  • dispatch: call the metadata endpoint to get simulation metadata (ae1054f), closes #2866

3.16.0 (2021-08-31)

Bug Fixes

  • deps: update dependency class-validator to v0.13.1 (#2894) (3676e59)
  • deps: update dependency nats to v2.2.0 (#2886) (7097edc)
  • deps: update dependency rxjs to v7.3.0 (#2895) (c01604b)
  • deps: update dependency stackdriver-errors-js to v0.10.0 (43451aa)
  • deps: update dependency tslib to v2.3.1 (#2888) (fc78756)

Features

  • dispatch: added dry run option to example simulation submission (1487880)
  • dispatch: added example simulation run for RBApy (277772e)
  • dispatch-api: set uris for metadata elements (96e94fe)
  • simulators: added ability to capture Python APIs in simulator specs (5ed44cb)

3.15.0 (2021-08-29)

Bug Fixes

Features

  • combine-service: updated to Biosimulators-utils with support for RBA models (610225b)
  • updated biosimulators documentation links to docs.biosimulatos.org (bfa49bb)
  • updated SBO for term for RBA (fc64418)

3.14.0 (2021-08-27)

Bug Fixes

  • combine-service: dont change field "abstract" to "_abstract" (591b0db)
  • combine-service: fix api client implementation (d313f1c)
  • dispatch-service: dont log error if job is not yet present (b80db71)
  • dispatch-service: fix url for posting metadata (a5926e7)
  • platform: correct url for metadata (c2a7a63)
  • platform: fix unterminated string literal (fe0343d)

Features

  • combine-service: isolating simulation execution into separate processes (9d23a5d)
  • combine-service: update combine api client (c1bb566)
  • dispatch-service: create handler to extract metadata (16b469a)
  • dispatch-service: process and create metadata for simulation runs (99df19d)
  • exceptions: change database errors to return 500 errors instead of 400 (7390b7f)

3.13.0 (2021-08-24)

Features

  • ontology: updated to KiSAO 2.27 (09ede72)

3.12.0 (2021-08-23)

Bug Fixes

  • dispatch-api: fields paramter is optional (c3863e3)

Features

  • dispatch-api: implement metadata endpoints (9d067e9)

3.11.0 (2021-08-22)

Features

  • combine-service: enabled NEURON, NetPyNe for simulation (19661df)

3.10.0 (2021-08-21)

Features

  • combine-service: added endpoint for low latency simulation (b44f5e3)
  • combine-service: added endpoint for low-latency simulations (931f3c7)
  • combine-service: added options to export simulation results in HDF5, zip formats (c0cd699)
  • combine-service: added simulator name to get simulaton tools endpoint (1f708dd)
  • combine-service: added test to verify simulator APIs (0bcaff3)
  • combine-service: pre-compiled Python code for faster initial calls (f368de9)
  • combine-service: updated AMICI, GillesPy2, libSBMLSim (fe8df2a)
  • combine-service: updated to KiSAO 2.26, BioSimalators-utils 0.1.105 (05b9dc5)
  • combine-service: updated to KiSAO 2.26, BioSimulators-utils 0.1.105 (74d0b36)
  • dispatch: added simulator names to simulation tools menu in run form (5170810)
  • ontology: updated to KiSAO 2.26 (f25f243)
  • simulators: added documentation for Python API conventions (60669be)

3.9.0 (2021-08-19)

Features

  • dispatch: added example run for MASSpy (a589891)
  • dispatch,ontology: started to add MASS, RBA formats (43a6153)
  • ontology: updated to KiSAO 2.25 (3fb5c54)

3.8.0 (2021-08-18)

Features

  • ontology: updated to kisao 2.26 (0f1f31a)

3.7.0 (2021-08-18)

Bug Fixes

  • update angular/cdk (c7a18c1)
  • deps: update dependency @openapi-contrib/openapi-schema-to-json-schema to v3.1.1 (#2799) (5d6453f)
  • deps: update dependency @sendgrid/mail to v7.4.6 (#2800) (1e83398)
  • deps: update dependency @typegoose/typegoose to v7.6.3 (#2803) (1a02d14)
  • deps: update dependency auth0 to v2.36.1 (#2823) (fa11231)
  • deps: update dependency cache-manager to v3.4.4 (#2804) (3c62abb)
  • deps: update nest (#2807) (875673f)
  • dispatch-service: added handling for case when no environment variables need to be set (b51418d)
  • platform: fix import of simulationrun metadata (fb85650)

Features

  • datamodel: add common api query parameters (c8bace5)
  • dispatch: added support for passing environment variables to simulators (107221a)
  • dispatch-api: add ability to get sparse simulationRuns (5570ebb)
  • dispatch-api: add endpoint for metadata (24ffa40)
  • dispatch-api: add tags, add ontology endpoint (d056b4a)
  • dispatch-api: create api model for metadata (#2815) (d55f7a5)
  • exceptions: add better handling of validation errors (e4e1986)

3.6.0 (2021-08-11)

Bug Fixes

  • dispatch: add logging when catching error (85fab6c)

Features

  • dispatch: added example runs for represillator model with SBML (3400fa1)
  • dispatch: added example simulation run for represillator model with OpenCOR (ebffbae)
  • dispatch: added example simulation runs with visuaulizations using SBGN PD maps (3c371e0)

3.5.0 (2021-08-09)

Bug Fixes

  • deps: pin dependency zone.js to 0.11.4 (51bd9c7)
  • dispatch: added timeout for loading similar algorithms (8c7a725)
  • dispatch: corrected display metadata loading indicator (346aaeb)
  • dispatch: fixed display of visualization loading indicator (59fcd98)

Features

  • dispatch: added buttons to publish projects (33c199a)
  • dispatch: added display of errors with metadata of COMBINE archives (41a0146)
  • dispatch: added support for XPP (3d108ad)
  • dispatch: improving capabilities when COMBINE service is down (dc9ca09)
  • dispatch: simplified designing 2D line/scatter plots with multiple curves (beab68e)

3.4.1 (2021-07-30)

Bug Fixes

  • deps: pin dependency @ngbmodule/material-carousel to 0.7.1 (0d1acde)
  • dispatch-api: send correct message when simulation status changes (a3c9c62), closes #2739

3.4.0 (2021-07-29)

Bug Fixes

  • dispatch: corrected processing of metadata while status is pinging (e29fb0e)

Features

  • dispatch: added example simulation run for activity flow diagram (f534c33)
  • dispatch: expanded support for connecting SED-ML to Vega (439bbeb)
  • ontology: updated SBO for additional framework terms (5eaa097)

3.3.0 (2021-07-23)

Bug Fixes

  • dispatch: hiding figures/tables section when there are no figures/tables (056caf8)

Features

  • dispatch,simulators: added documentation about generating data visualizations (0066522)
  • making creation data metadata optional (7812d65)

3.2.0 (2021-07-22)

Bug Fixes

  • dispatch-api: change path from 'run' to 'runs' (ead8d80)

Features

  • dispatch: improved Vega error handling (56a1e0c)
  • dispatch: updated example runs for new vis and metadata (1683451)
  • platform,platform-api: platform gets projects from api (f0b010d)
  • simulators: added documentation about recommendation to use Identifiers.org URIs (5445b08)

3.1.0 (2021-07-19)

Bug Fixes

  • deps: pin dependencies (5c762b6)
  • deps: update nest monorepo (790aa52)
  • dispatch: fixed handling of query arguments to run simulation route (546c49b)
  • simulators: reenabling display of simulator validation test results (902bc93), closes #2696

Features

  • dispatch: added 1D histogram plot (379e0a7)
  • dispatch: added 2D heatmap data visualization (147b6ad)
  • dispatch: added ability to add files to COMBINE archives (c05631e)
  • dispatch: added exporting user-configured histogram viz to Vega (6342e44)
  • dispatch: added Vega export for 2D heatmap, improved visualization form validation (784917f)
  • dispatch: added Vega export for 2d line/scatter plot (8f2cff0)
  • dispatch: improved plotting (852545b)
  • dispatch: linked Vega signals to attributes of SED-ML simulations (88a68c3)
  • dispatch: linking published figures/tables to displayed visualizations (44c810a)
  • platform: implement viewing a project (0ad9af3)
  • platform-api: add skeleton implementation (0758052)

3.0.2 (2021-07-13)

Bug Fixes

  • mail-service,dispatch-service: fix nats-server connection (9143d0c)

3.0.1 (2021-07-13)

Bug Fixes

3.0.0 (2021-07-13)

Bug Fixes

  • mail-service,dispatch-service: fix import of http module (805e48f)

Features

  • simulators-api: add a query argument to include the results of the validation (710be08), closes #2668

BREAKING CHANGES

  • simulators-api: validation data is no longer returned by default. A Query argument is needed to include the validation information

2.5.2 (2021-07-13)

Bug Fixes

  • type and build fixes (6812bd0)
  • dispatch-api: fix error with parsing outputIds (9fac99f), closes #2683

2.5.1 (2021-07-09)

Bug Fixes

  • simulators-api: Allow for date based versions (0c8fb8d), closes #2681

2.5.0 (2021-07-09)

Bug Fixes

  • dispatch: downloading created COMBINE/OMEX archives (03895bf)
  • correcting size of form fields (ae69630)
  • shared-exceptions: include error metadata in the "meta" output (2be0178)

Features

  • combine-service: adding support for creating steady-state analyses of logical models (a9e6667)
  • combine-service: updating to biosimulators-utils 0.1.93 (ca0a21e)
  • shared-exceptions: add validation pipe error factory (35edb4d)

2.4.0 (2021-07-08)

Bug Fixes

  • combine-service: add protocol to server in API spec (bcf4119)
  • combine-service: debugged specifications (f8b9420)
  • combine-service: fix api spec (ebab457)
  • platform: enable strict template checking, fix type errors (9facdb1), closes #2185

Features

  • combine-service: add combine-service api client library (bfa25b8)
  • dispatch: added example simulation run for GINsim (3e639b3)
  • dispatch: added example simulation runs for GINsim, LibSBMLSim (06ad0a4)
  • dispatch: adding support for GINML, ZGINML to COMBINE archive creation and execution (9f949e5)
  • dispatch,ontology: add terms for GINsim format (22d8a7b)
  • ontology: updating to KiSAO 2.19 with terms for logical modeling (c47e63b)
  • ontology,combine-service: update to KiSAO 2.20 (fadf3da)

2.3.0 (2021-07-02)

Features

  • dispatch: Added tab to simulation run page to display metadata about the simulation project (#2667) (dde87fa), closes #2661

2.2.1 (2021-07-01)

Bug Fixes

  • dispatch: fix example simulation runs (60d91c1), closes #2653
  • simulators-api: fix getting latest version (4594c96), closes #2664

2.2.0 (2021-06-30)

Bug Fixes

  • dispatch: correct integration between simulation results and SED plots (0bab60f)
  • dispatch: download file instead of redirect (cd2840d), closes #2435
  • dispatch: use correct api to get simulator info (1e66f1f)

Features

  • add some shared endpoints (567e4c2)
  • auth-client: Cache tokens locally (f53c9f8), closes #2503
  • auth-common: add util functions (e0ac842)

Performance Improvements

  • dispatch-service: use /local as the singularity cache/working directory (c63b58c)

2.1.0 (2021-06-18)

Bug Fixes

  • dispatch-service: remove check for process flag (f7f88cc), closes #2577

Features

  • dispatch-api, dispatch-service: add status reason to datamodel (ca9bcb6), closes #2441

2.0.0 (2021-06-17)

Bug Fixes

  • dispatch-api: bind class to this variable in map (b4bb3ca)
  • dispatch frontend uses the updated api parameter (#2636) (a13779c), closes #2635

Features

BREAKING CHANGES

  • dispatch-api, dispatch-service: Dispatch API no longer has endpoints for creating or updating "Result" objects. The output of the results endpoints are updated to include information about type and shape of the data. The parameter "sparse" has been changed to "includeData". The datamodel for results has been adjusted to include all outputs, not just reports. "reports" has been renamed to "outputs"

1.0.0 (2021-06-16)

This is an arbitrary starting point for tracking changes and versioning. It should not be considered as the "first release".

Bug Fixes

  • bash script (866b58a)
  • add check for large files downloading (ca10aa5), closes #2536
  • bring inline with datamodel (af53a54)
  • change url to download results (3d264d4), closes #2561
  • check job status after completion (c16649c)
  • cleanup logs (fbd330f)
  • correct value for constant (e2d3a68)
  • fix error in reading port (e1f6fb9)
  • fix logs and context buttons (777e8e8), closes #2543 #2540
  • fix redis queue and port (5f33a19)
  • fix s3 key for downloading outputs (f585a9a), closes #2622
  • fix spelling of library (a471e95)
  • fix test (6f236df)
  • fix test (6af0ca8)
  • lint fix (a26c24b)
  • order of operations for creating results (eac31e0)
  • propely set name and filetype of outputs (951c239)
  • Remove bad library import (ecc86fa), closes #2420
  • remove xdg runtime directory (f5ec15b)
  • resolve build errors (6691ebe)
  • typo in return statement (1f6c4fc)
  • update default stoage URL (f9b0d75)
  • update logs (818a0c3)
  • update sbatch memoy amount (b9026f9)
  • update sbatch script to use custom module (0ef1c52)
  • use job status to determine completion (adb12a0)
  • apps/frontend: relative import (3854f27)
  • auth: check for logged in before intercepting (7c22a19)
  • auth: Check for username correctly (05996b3)
  • disatch: Fix open api schema (ff15503)
  • dispatch: Fix observable piping (34e7086)
  • dispatch: parsing results accounts for quotes (d055a7b), closes #2459
  • dispatch: patch error handling (d2d98e5)
  • dispatch: remove bad environment variables (3c31b7d), closes #2476
  • dispatch: Simulation results not saved for some simulations and overall status doesn't reflect such errors (#2428) (acd2dff), closes #2416
  • use https for auth0 image (19a4dcc)
  • forms: connect taxon form properly (a4088f7)
  • forms: fix reference form implementation (5b3eba4)
  • forms: fix some taxon form details (8802ced)
  • forms: fix tags form (b60b99c)
  • forms: fix validation error with taxon form (6cb2d43)
  • forms: Form does not scroll over topbar (70f3275)
  • forms: set file form disable properly (c523d0e)
  • gaurds: Gaurd loads underconstruction pages by default (9f7a810)
  • grid: grid work with async resources (d621cd3)
  • interceptor: API token, error handling (78be137)
  • interceptor: Fixed a bug in the error handling of the interceptor (1397c96)
  • models: Edit component calls subscribe (50f15ac)
  • navigation: get username via async (7415eba)
  • navigation: have navigation work with async (0da33ea)
  • polyfill: add back polyfill (30e9c1d)
  • resource service: add query params to read (d1d7d38)
  • resources: Move more functionality into abstract class (5e94323)
  • serializer: fix private public being flipped (035241f)
  • serializers: improve serializers (0d3f004)
  • serializers: user serializer returns none for '' (221ce41)
  • services: Dont cast http reponse to resource (b20e69d)
  • simulations: fix async view (d2cad0f)
  • tests: fix common test issues (61c7621)
  • tests: fix common test issues (0c4e5f3)
  • user: profile edit component properly creates user (0bed682)
  • visualizations: fix licence view (f5d9973)

Features

  • add client library (820647b)
  • add config for queue (c7ec4a1)
  • add hsds client module (1730521)
  • use org for getting latest simulator (2f7c503)
  • api: add config to api (931dcf5)
  • api: add crud skeleton for routes (64fce18)
  • api: add open api spec generation (659f8b4)
  • author form: build out author form (afe666a)
  • datamodel: add gaurds (2ffdf04)
  • datamodel: add more of the core datamodel (9b28f83)
  • datamodel: add properties to format (67b024c), closes #462
  • datamodel: add url to ontology (3c8a169)
  • datamodel: redefine core objects as set of attriutes (95ea0a7)
  • datamodel: redfine core resources as primary and secondary (dd2fec4)
  • dispatch: add a dispatch service (152b3b0)
  • errors: add default errors component (a10b927)
  • errors: Create 404 component (e1c7d33)
  • errors: Create errors module (7e3cac4)
  • errors: Create under construction component (5d2fbe1)
  • errors: slight changes to underConstruction (bb06012)
  • forms: add a component for file inputs (e843f87)
  • forms: add abstract array subform (1d70e47)
  • forms: add authors and identifiers components (d2e35e8)
  • forms: Add identifier form control (dd80d37)
  • forms: add name form control (8557559)
  • forms: add required validator to fields (ceaacb5)
  • forms: add resource form skeleton (e7a56d5)
  • forms: add taxon form (48a2e86)
  • forms: add to resource form implementation (dc0b9ed)
  • forms: add username form (7ba4e81)
  • forms: create a model form (353d2ab)
  • forms: Create descriptions form control (87b0fdd)
  • forms: Create edit-preview component (5177f05)
  • forms: create model format form (af0ad55)
  • forms: enable access form component (741afa3)
  • forms: Enable Drag/Drop (799147b)
  • forms: Finalize author form (3f4f86c)
  • forms: Generalize single field controls (0da8122)
  • forms: implement licence form (2d2d9b1)
  • forms: implement refrences form (122fa33)
  • forms: implement resource form (85e89ea)
  • forms: implement tags form (0b1e480)
  • forms: improve disable handling (88cace8)
  • forms: styling (32044ef)
  • home: Add sponsors section (8f84a67)
  • logging: Added logging (18476ca)
  • login: add styling (642a71c)
  • login: redirect works (eb05030)
  • mateiral: add a material topbar (4325dcc)
  • models: add query-options model definition (d628289)
  • projects: add view project (dab3c59)
  • pwa: Add pwa capabilities (27b9050)
  • resources: Resources now have owner embedded (f03c30b)
  • serializers: serializers read files properly (c0eb5c1)
  • service: Breadcrumb service generates breadcrums (68efc1a)
  • services: add config service (98ed473)
  • services: add file service (0538686)
  • services: add test organism to metadataservice (91f2503)
  • services: Resource services return new model (0c32ba5)
  • shared: add an authentication library (904cd59)
  • shared: add fields to remote file (b85ff9d)
  • shared: add more model serializing (b06129d)
  • visualization: More flexible 2D visualization to better match needs of SED-ML L1V3 and BioModels (31c96de)
  • add construction gaurd in prodction mode (84708a2)
  • create a debugger component (fd47c37)
  • shared: add under constrcution gaurd (d931f6d)
  • shared: Remote file has a method to create from File (f3360cf)
  • simulations: Simulations now have embedded models (4dd512b)
  • users: Add different snackbars (056ffe2)
  • visualizations: add view async capapbility (d2eb414)

Reverts

  • "Formatted Files. [skip ci]" (0414aca)
  • Revert "debug redis host" (7264f87)
  • Revert "Feat(Combine-serive): Update API Specification" (7ada4ce)
  • Revert "Updated Ontologies" (aab6f70)
  • Revert "Bump @sendgrid/mail from 7.4.1 to 7.4.2 in /biosimulations (#1975)" (#1979) (a96e0ea), closes #1975 #1979
  • Revert "Bump @nrwl/cli from 10.4.1 to 11.0.20 in /biosimulations (#1855)" (#1860) (b7d637e), closes #1855 #1860
  • Revert "merging enumerations of simulation status; aligning names of properties 'resultsSize' and 'resultSize'" (08e96f2)
  • Revert "Revert "styling nested lists and lists after paragraphs"" (16a2d5b)
  • Revert "Revert "adding management for app-specific configuration (e.g,, appName, logo, etc."" (1c6190a)
  • Revert "Revert "adding documentation"" (f71cfcd)
  • Revert "Revert "editing help"" (4aea612)
  • Revert "Revert "adding documentation of supported SED-ML features"" (32beb34)
  • Revert "changing completed to updated" (d9fe18e)
  • Revert "update to angular 10" (e1b9fcf)

  • Revert "Bump husky from 4.0.1 to 4.0.5 in /CRBM-Viz (#290)" (4dd2cc3), closes #290

  • feat (dispatch-api): remove download endpoint (785ad27)

  • feat (dispatch) : Change datamodel of returned results (ba42dcc)

BREAKING CHANGES

  • The /download endpoint has been removed. Should be replaced by /results/download
  • The results are now returned as an array of objects (AOS) rather than an object of arrays (SOA)
Last update: 2023-04-12