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Dynamic services to use storage (#334)
* 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
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.travis.yml

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# wait for postgresql to shutdown
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- while sudo lsof -Pi :5432 -sTCP:LISTEN -t; do sleep 1; done
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install:
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install:
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- pip install --upgrade pip wheel setuptools && pip3 --version
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- pip3 install pytest-travis-fold
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- pip3 install packages/s3wrapper[test]
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- pip3 install packages/simcore-sdk[test]
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- pushd services/director; pip3 install -r requirements/ci.txt; popd

Makefile

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TEMPCOMPOSE := $(shell mktemp)
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export PYTHONPATH=${CURDIR}/packages/s3wrapper/src:${CURDIR}/packages/simcore-sdk/src
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all:
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@echo 'run `make build-devel` to build your dev environment'
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api/specs/director/v0/openapi.yaml

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$ref: '../../shared/schemas/health_check.yaml#/HealthCheckEnveloped'
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$ref: '../../shared/schemas/health_check.yaml#/components/schemas/HealthCheckEnveloped'
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default:
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$ref: '../../shared/schemas/error.yaml#/ErrorEnveloped'
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$ref: '../../shared/schemas/error.yaml#/components/schemas/ErrorEnveloped'
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summary: Starts an interactive service in the oSparc platform and returns its entrypoint
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operationId: running_interactive_services_post
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parameters:
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parameters:
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- $ref: '#/components/parameters/UserId'
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components:
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UserId:
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in: query
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name: user_id
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description: The ID of the user that starts the service
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required: true
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schema:
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type: string
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example: asdfgj233
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api/specs/shared/schemas/error.yaml

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ErrorEnveloped:
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- error
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schemas:
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error:
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$ref: '#/ErrorType'
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ErrorType:
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type: object
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required:
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properties:
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message:
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description: Error message
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type: string
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errors:
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type: array
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items:
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properties:
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code:
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type: string
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description: Server Exception
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status:
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description: Error code
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type: integer
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example: 404
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required:
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data:
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default: null
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error:
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ErrorType:
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type: object
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required:
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- status
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- message
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properties:
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message:
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description: Error message
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type: string
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example: Unexpected error
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errors:
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type: array
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items:
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properties:
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code:
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type: string
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description: Server Exception
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status:
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description: Error code
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type: integer
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example: 404
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HealthCheckEnveloped:
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type: object
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required:
4-
- data
5-
- error
6-
properties:
7-
data:
8-
$ref: '#/HealthCheckType'
9-
error:
1+
components:
2+
schemas:
3+
HealthCheckEnveloped:
104
type: object
11-
nullable: true
12-
default: null
13-
14-
HealthCheckType:
15-
type: object
16-
properties:
17-
name:
18-
type: string
19-
example: director service
20-
status:
21-
type: string
22-
example: SERVICE_RUNNING
23-
api_version:
24-
type: string
25-
example: 1.0.0-dev
26-
version:
27-
type: string
28-
example: 1dfcfdc
5+
required:
6+
- data
7+
properties:
8+
data:
9+
$ref: '#/components/schemas/HealthCheckType'
10+
error:
11+
nullable: true
12+
default: null
13+
14+
HealthCheckType:
15+
type: object
16+
properties:
17+
name:
18+
type: string
19+
example: director service
20+
status:
21+
type: string
22+
example: SERVICE_RUNNING
23+
api_version:
24+
type: string
25+
example: 1.0.0-dev
26+
version:
27+
type: string
28+
example: 1dfcfdc
+10-13
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,11 @@
1-
Response204Enveloped:
2-
type: object
3-
required:
4-
- data
5-
- error
6-
properties:
7-
data:
1+
components:
2+
schemas:
3+
Response204Enveloped:
84
type: object
9-
nullable: true
10-
default: null
11-
error:
12-
type: object
13-
nullable: true
14-
default: null
5+
properties:
6+
data:
7+
nullable: true
8+
default: null
9+
error:
10+
nullable: true
11+
default: null

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