Modeling: Primitives and simple operations #9
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mguidon
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pcrespov
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in pcrespov/osparc-simcore
Sep 6, 2018
Director sdk closes ITISFoundation#197
oetiker
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in oetiker/osparc-simcore
Oct 16, 2018
Feature/ITISFoundation#233 api sharing
sanderegg
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Nov 16, 2018
* Fix pytest on travis * Added SMTP_HOST and SMTP_PORT to the docker-composes * No more fake files * Fixed webserver<->storage specs * File Picker get nodeModel and projectId * Get MyDocuments * Trying to upload files * fix swarm config for storage * Increased PLATFORM_VERSION to 3.19 * Revert "Increased PLATFORM_VERSION to 3.19" This reverts commit cd37313. * Increased PLATFORM_VERSION to 3.19 * upgraded openapi code generator re-generated storage client sdk * go back to 3.2.3 * renamed package name * fixed crash when no datcore present * fixed openapi definition for getting locations - was not returning enveloped response * improved script to automatically remove output.yaml * modified openapi to specify it actually returns envelopes re-generated client * created sample file for testing client * fixed usage of upload link * defines link as required * removed python notebook * removed log * changed dependency from s3wrapper to storage client sdk * make use of Path to ensure correct / * change name of package to follow conventions * renamed requirements for production * code cleanup * added necesary config entries * moved includes to fixtures to top'level conftest * pylint * fixed storage setup script to copy the openapi correctly * fixed dependencies to servicelib * fixed naming * added logs * added exception for storage connection error * return value of location id is an integer not a number * strip " from none * added fixture to start storage servicemoved minio out of the docker stack so that pre-signed urls are correctmade filemanager asynctest filemanager complete and functional * filemanager tests are passingadded exceptions to handle storage server errors * added configuration for store and bucket * moved fixtures to conftest added teardowns for DB added external minio to get functional pre-signed keys * added new way of creating file id * parts of nodeports test passing made parts async * added more helpers functions for testing * fixes the warnings regarding ssl * refactoring fixed file_uuid fixture * fixed await missing * refactoring storage fixture fixed issues * missing files * fixed tests for getting files and values from previous nodes things are more flexible * nodeports tests are passing again * download using async library aiofiles * pylint * code cleanup * pylint * updated code generator to latest version * removed usage of prance to resolve openapi as this is now fixed by fixing the openapi specifications updated the storage sdk client code removed wrong nullable entry where a non null response is expected set openapi schema file to include the components and schemas namespaces to fix validation error about unknown schema fixed all references by using / after the # * changed image to use for testing * replace the minio fixture with the new external to the docker-compose stack * fixed endpoint without scheme * storage build for tests * update docker-compose on travis * fix issue with not creating parent paths * pylint * fixed issue with windows invalid path * pylint * Little fixes (#9) * update docker-compose on travis * fix issue with not creating parent paths * pylint * fixed issue with windows invalid path * pylint * fix deps for mock * try to fix travis hang * pylint * try to satisfy travis with log output * fixed dependencies of sidecar * another travis test * fixed dependencies * re-arranging nodeports * re-arranged test folder * fixed installation dependencies * fixed imports * re-arranged nodeports for simplicity * use the latest minio only * removed the timeout * wrap async calls in sidecar * change configuration to STORAGE_ENDPOINT * Slightly change API * updated the client code * pylint * adapted node ports to new storage api * fixed setting up of storage enpoint in test * fixed dependencies. without this requirements, the pdb debugger does not stop * makefile cleanup * adapted to new API * fixes return value * added mark as pytest asyncio * set as internal port * pylint * only build storage * export DOCKER_GID before building storage * wrong env * fixes tests * Revert back to old api * Remove unused field * FakeData updated to new data structure * minor * presignedURL request fixed * minor * minor * cleanup * updated storage client sdk * reverted storage api * mark asyncio tests as async * removed usage of psycopg2 * remove location from fileuuid * Merge sandereggs changes * removing SIMCORE_PIPELINE_ID * location name is not part of file ID anymore * fix issues with openapi files * Forgot those * refactoring * allow to also change inputs * added storage to the devel environment added STORAGE_ENDPOINT to the config variable * simplified notebook client * code refactoring * renamed * Fix rerouting to storage * fixed typo * renamed folder * added custom.js to notebook to prevent opening in a new tab * yaml, we said yAml!! * user id needs to be passed by the director * only allow doing stuff in the notebooks folder * Remove bucket name from file_uuid. It is already defined by the location_id * Make api for copy more clear * Make api for copy more cleard-s * improved theming * added comments * Implements copy datcore->s3 * removed bucket from file id * minor * try pytest fold * updated director api to pass user id * re-generated director server stubs * refactoring of producer pass user id to dynamic services * re-generated director client sdk code * fixed typos, variable checks * datcore fakedata updated * registry proxy is now async * producer now async * handlers now using async * eslint * fix test * Adds test for file_uuid creator * fixed configuration of director sdk * ISSUE: fixed regular expression in generated sdk code * Squash from PR#324 webserver uses apihub Squashed commit of the following: commit eb33599 Merge: a715899 f7eec98 Author: Pedro Crespo <[email protected]> Date: Wed Nov 14 11:41:20 2018 +0100 Bad merge Conflicts: services/director/requirements/base.txt commit a715899 Merge: 0806917 b1f7ad9 Author: Pedro Crespo <[email protected]> Date: Wed Nov 14 11:36:07 2018 +0100 Merge branch 'is309/webserver-uses-apihub' of github.com:pcrespov/osparc-simcore into is309/webserver-uses-apihub commit f7eec98 Merge: 0806917 b1f7ad9 Author: Pedro Crespo <[email protected]> Date: Wed Nov 14 11:36:07 2018 +0100 Merge branch 'is309/webserver-uses-apihub' of github.com:pcrespov/osparc-simcore into is309/webserver-uses-apihub commit 0806917 Merge: 89563a3 ed07bfd Author: Pedro Crespo <[email protected]> Date: Wed Nov 14 11:35:25 2018 +0100 Merge branch 'master' into is309/webserver-uses-apihub commit ed07bfd Merge: 0156ec8 c258483 Author: Pedro Crespo <[email protected]> Date: Wed Nov 14 11:31:37 2018 +0100 Merge remote-tracking branch 'upstream/master' commit c258483 Author: Tobias Oetiker <[email protected]> Date: Wed Nov 14 11:29:25 2018 +0100 Build Environment Fixes (#314) * make swarm work on osx * use compose to create input for docker stack * have a separate target for launching the qxbuild * do NOT put explicit dns into the compose file!!! rather make sure the /etc/resolve.conf on the host where docker is running is setup correctly! * do not rely on boot.sh exec permissions when starting sidecar * allow override of REGISTRY_URL from .env * better targets for fontent dev * Working Makefile for PowerShell commit b1f7ad9 Merge: 89563a3 ff0ac55 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 22:11:36 2018 +0100 Merge branch 'master' into is309/webserver-uses-apihub commit 0156ec8 Merge: e71ed59 ff0ac55 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 21:31:06 2018 +0100 Merge remote-tracking branch 'upstream/master' commit 89563a3 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 19:26:45 2018 +0100 Fixes retrieving openapi to webserver. commit c166bc0 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 18:08:39 2018 +0100 Fixes makefile filter (see previous commit) Removed deprecated modules from merge Fixed container_environ fixture Added +x to entrypoint.sh otherwise container does not have execution permissions commit 05d5423 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 17:42:45 2018 +0100 Fixes bad merge in test_reverser_proxy. Disabled web/server pylint from makefile since test_package has a linter test and single-file pylint checks produces false positives with relative imports commit 63df90c Merge: bd48b1e e71ed59 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 17:29:43 2018 +0100 Merge branch 'master' into is309/webserver-uses-apihub commit e71ed59 Merge: 5320cef 2fbeba2 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 17:27:33 2018 +0100 Merge remote-tracking branch 'upstream/master' commit bd48b1e Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 17:25:09 2018 +0100 Fixes login tests. Added new variable in config commit f85a452 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 17:19:29 2018 +0100 Replaced main.disable_services by "enabled" flags in every service commit 376f652 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 16:40:25 2018 +0100 Fixes enveloped schemas to have null error. Modifies the test_conventions... to adapt to new criteria commit c034676 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 16:31:26 2018 +0100 Added custom variables (OSPARC_SIMCORE_REPO_ROOTDIR) for the config file Fixes config folder key commit f1a0a42 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 13:35:42 2018 +0100 Fixed linter error commit 5161825 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 12:01:37 2018 +0100 fixes on schema my.yaml test failures commit 0fbcd81 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 11:38:58 2018 +0100 Removed deprecated tests commit c774d67 Merge: 1df73de 359a12c Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 11:35:52 2018 +0100 Merge branch 'is309/webserver-uses-apihub' of github.com:pcrespov/osparc-simcore into is309/webserver-uses-apihub commit 359a12c Merge: 6b35214 ff41cf4 Author: Pedro Crespo <[email protected]> Date: Tue Nov 13 11:32:42 2018 +0100 Merge branch 'master' into is309/webserver-uses-apihub commit 1df73de Merge: fec4dd3 6b35214 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 16:49:09 2018 +0100 Merge branch 'is309/webserver-uses-apihub' of github.com:pcrespov/osparc-simcore into is309/webserver-uses-apihub commit 6b35214 Author: Pedro Crespo-Valero <[email protected]> Date: Mon Nov 12 16:01:00 2018 +0100 complement previous commit commit 352fc5e Author: Pedro Crespo-Valero <[email protected]> Date: Mon Nov 12 15:58:35 2018 +0100 Upgrade requests to version 2.20.0 to solve vulnerability alarm commit 19c7596 Merge: 5746dd5 f51d68b Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 15:56:31 2018 +0100 Merge branch 'master' into is309/webserver-uses-apihub commit 5746dd5 Author: Pedro Crespo-Valero <[email protected]> Date: Mon Nov 12 15:46:56 2018 +0100 Removed resouces_keys commit fec4dd3 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 15:25:04 2018 +0100 Fixes login ests commit 26845b1 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 15:13:57 2018 +0100 Removed application_keys.py commit b3d7d9c Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 15:13:57 2018 +0100 Removed application_keys.py commit 984c9b8 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 15:09:59 2018 +0100 Cleanup rest. test_rest running commit 4597c24 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 12:16:07 2018 +0100 Gathered all director subsystem's modules under a folder commit a815a3e Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 11:58:46 2018 +0100 Renamed comp_backend as computation Minor commit 0ff6c01 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 11:57:24 2018 +0100 Split sockets subsystem into setup and handlers Added s3 subsystem commit 5098583 Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 10:55:20 2018 +0100 Adapted configurations to latest schema. Added environs to docker-compose and removed from .env-devel hosts and ports (should be hard-coded in docker-compose) commit cff674b Author: Pedro Crespo <[email protected]> Date: Mon Nov 12 10:54:54 2018 +0100 Synced some requirements commit de4f9dc Author: Pedro Crespo <[email protected]> Date: Sat Nov 10 21:21:28 2018 +0100 - every subsystem defines its own config section: computation, db, email, rest, director . All have their own *_config.py - created directory submodule and its config - added tests for config sections - renamed settings as application_config - renamed computational_backend as computation commit 4bde625 Author: Pedro Crespo <[email protected]> Date: Fri Nov 9 20:10:34 2018 +0100 WIP commit 5320cef Merge: cf6c63a 062f221 Author: Pedro Crespo <[email protected]> Date: Fri Nov 9 17:17:34 2018 +0100 Merge remote-tracking branch 'upstream/master' commit cf6c63a Merge: 4a8c093 63e662c Author: Pedro Crespo <[email protected]> Date: Fri Nov 9 11:09:51 2018 +0100 Merge remote-tracking branch 'upstream/master' commit 4a8c093 Merge: 0fd2975 1a3ed38 Author: Pedro Crespo <[email protected]> Date: Wed Nov 7 11:57:52 2018 +0100 Merge remote-tracking branch 'upstream/master' commit 0fd2975 Merge: d423dcc 8d7d44f Author: Pedro Crespo <[email protected]> Date: Mon Nov 5 10:24:49 2018 +0100 Merge remote-tracking branch 'upstream/master' commit d423dcc Merge: 6ca6aad dfdd594 Author: Pedro Crespo <[email protected]> Date: Fri Nov 2 14:06:23 2018 +0100 Merge remote-tracking branch 'upstream/master' commit 6ca6aad Merge: e733846 cae4fb1 Author: Pedro Crespo <[email protected]> Date: Wed Oct 31 14:33:37 2018 +0100 Merge remote-tracking branch 'upstream/master' commit e733846 Merge: 9e40d37 77d6ac1 Author: Pedro Crespo <[email protected]> Date: Wed Oct 31 13:36:25 2018 +0100 Merge branch 'master' of github.com:pcrespov/osparc-simcore commit 9e40d37 Merge: 65f510c 0b60f46 Author: Pedro Crespo <[email protected]> Date: Tue Oct 30 18:53:50 2018 +0100 Merge remote-tracking branch 'upstream/master' Pull * updated storage configuration * move the webserver-storage api to apihub * Create bucket if not yet there * fixes bad merge * added director handlers added oas specs * linked director handlers creating director test * useless test * added director client session * added version to director schema fixed typo * bad merge * removed registry_api * removed userid from webserver api * changed call to startDynamic stopDynamic to go through the rest API instead of websockets * refactoring * fixed version of path use isfunction instead of ismethod to find handlers * Feature/fe dsm (#15) * Pylint * Add reference osparc.itis stack template * fixed call to API by explicitely using query parameters * the server side does not like the format field... * refatoring * call forwarding now also forwards the query parameters * removed logging * added workbench json and its converted openapi counterpart added route to start pipeline * implementation of new route * comment out code to fix cyclic import * fix bad merge * eslint * pylint * bad merge * disable old start_pipeline * bypass validation * regenerated client sdk * store now contains the id instead of the store name * added async sleep when waiting for service start fixed looking for service dependencies * fix bad merge * bad merge * pass the user id to the sidecar * fix test * use env variable instead of hard-coded host/port * add storage endpoint env to director so it can pass it on add storage endpoint to sidecar so it can use it * renamed to test_package * mapping of routes working * pylint
ignapas
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May 26, 2020
* Fix for is1499 * fix e2e (#9) * Added README to e2e testing * Solved bug with rotating Idle icon * Disabled no-eq-null rule to be able to check for null or undefined * Added e2e debug config to vscode templates. Moved gitignores to new file * Allowed new gitignores * Continue button in feedback dialog now closes the window Co-authored-by: Odei Maiz <[email protected]>
GitHK
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Oct 27, 2021
* there seems to be an issue elsewere * fixed issue when booting * enabling debug boot * injecting pahts to all containers * all declared volumes are removed as well * fixing dy-sidecar unit tests * dv2 added volume creation and removal for dy sidecar * forarding pgsettings to dybamic-sidecar * setting refactoring * volumes are properly mounted on the spec * adding additional setup elements * starting direcotry watcher * adding module to properly manage volumes * fixed some tests * created new directory * using correct password * better error message * codestyle * extended tests for the API * refactor renames * attached nodeports pulling * adding permissin changes * semplified interface for saving and restoring the service state * using new api interface * is no longer set to fail * refactored * raising error now * fixing tests * added data_manager integration * added tests for mounted_fs * added missing env var and refactor * fixed API call to save and restore state * pylint * fixing tests * fix mounted_fs and volumes generated * refactored volume resolve and mounting * added missing env paths * fixed an issue with initialization * fixed issues with permission changing * added more comments * rename refactor * changed debug message * minor refactor * added utility to run on threadppols * using not blocking calls * adds API for nodeports push and pull * fix codestyle * updated opeanpi specs for new entrypoint * updated webserver ospeanpi spec * always return size in bytes of the trasnferred data * updated openapi.json * exposed retrieve to frontend * ensures clean shutdown in call cases * split nodeports from state saving * fixing codestyle * refactor * codeclimate * codestyle * fixed version parsing * Feature/dynamic retrieve (#8) * minor * refactoring * bumped version * bumped service version * composing correct url * version bumped * revert change * computeServiceV2RetrieveUrl (#9) * computeServiceV2RetrieveUrl * minor * updated openaipi specs * updated requirements * added new webserver entrypoint * added retrieve api to director-v2 * fixed director-v2 tests * fix bug * inverted oder * sending in the correct format * faster booting of dy-sidecar * removed todos * update policy timeout * fixed depenencies after merge * using appropriate images for testing * pylint * storage is now connected for this test * fix status url * fixed port forwarding issues * fixed broken test * removed dangerous code * updated openapi.json * minor refactor * further refactoring * refactor * further refactoring * shared functions refactored * refactor * added save_to option to datamanager.pull * refactor * added dependencies for testing * aded nodeports integration test * removed unsued plugin * trying to fix test in CI * refactor API interface * updated API inteface after change * moving to fixure * added more information * using nodeports execption * rename function * mocked api removed, no requests are fowarded here * refactor * renaming function * updated docstring * updated description * update comment * fix comment * updated _meta.py * revert to old version * adding watchdog * added missing requirement * added missing requirement * removed test uncertanty * enhanced test slightly * fixed broken endpoint * adding some debug messages * updated openapi specification * expadning fixture to support multiple versions * added better description * typing * removed comment * added timeouts * using ByteSize * renamed * renmed save_state to can_save * reverting change * more renaming * renaming restore * renamed endpoints * updated openapi.json * @sanderegg fixing in all Dockerfiles * migrated to dataclass * better debug messages * fixed docstring * [skip ci] no ci when pushing * making it easier to debug * trying to give nodeports more time * put back missing parameter * putting back option * restored missing API * fixed typing * replaced with 3.8 version * typo * using statues from starlette * making it run in development * fixed import issue * only log keys * aded status retrying * ading retries on status and retrieve * refactor * renaming and refactoring * renamed again * removing dependency bump * reverting * added minio * added extra comments * added more assersions * added more debug prints * adding more infomation in logs * more explicit debug message * added sleep to make sure data is available * adding more information to make it easier to debug * tring to trigger CI again * reafactoring * refactor * used for testing, leaving it in * added new container logs dump for simpler debugging * dumping logs twice * adding logs debug * updated return type * logs from containers on fail * using version with more debug options * bumped expected version in workbench * better error message and explaniation * even more debug information * put back original check * added separators * removed space * trigger CI again * bumping timeout * prining data for all containers * fix issue * bumping dy_static_file_server version * updated versions in workbench * fixing python-lining CI * reverted changes * debug help * addresses an issue with stopping * fix error * replaced logging. with logger. * adding more debug messages * adding healthcheck to traefik * enabling logs from traefik * adding more logging * adding more logs * raising attempts 15 minute timeout * adding better debug messages * changed the dafults to something else * added logging when data is not found to be upoaded * updating logs on function * fixes a race condition when saving ports in parallel * reverting changes * changed endpoint to make it more readable * removed client-sdk references * migrated nodeports implementaiton * archiving folders is now done in parallel * fix import issue * some missing types * typing * fix pylint * checking how much the test lasts * fixing timeout for test * added faster bailout * making bigger case start first * adding debug flags to detect hangs * reduced timeout to a reasonable value * added port forward for proxy to test * making tests more reliable * extended logging * pylint Co-authored-by: Andrei Neagu <[email protected]> Co-authored-by: Odei Maiz <[email protected]>
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The framework provides simple modeling operations within the 3D window:
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