Promote to PROD #354
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Promote to PROD #354
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* Pivotal ID # 173457302: RelPath Calculation In an accession with several number groups only the last will be used * Pivotal ID # 173457302: RelPath Calculation Improve regex
* Pivotal ID # 173750220: Author TSV Serialization Fix serialization for subsections without accession * Pivotal ID # 173750220: Author TSV Serialization Improve test cases
* Pivotal ID # 172817960: Resubmit Notification - Changes in the architecture to use queues instead of events for notifications - Get the extended submission from the service instead of passing down the elements in the event - Add logic to load different templates based on the submission version - Create/update the RT ticket depending on its existence - Add testing - Remove unused code - Update the handlers application properties file
- removed superuser flag
- changed file api - updated dependencies
- added new query to reduce overload - removed transactional for submission submiter
…251) Improve submission full graph performance
* Pivotal ID # 172817960: Resubmit Notfication - Create an extended user endpoint - Use the endpoint to get the user information in the notifications side
* added custom loading strategy
* Pivotal ID # 172817960: Resubmit Notification - Move security notifications to queues based mechanism - Create an independent module to publish messages to the queues - Move all the notifications logic to the notifications module - Improve the handlers application configuration - Remove unnecessary code related to the observable logic and unused events - Fix broken tests and build
* simplified relpath calculation extrategy
- Fix validation errors on project AccNo template - Improve class readability - Add unit tests
* separated submission and processing steps * code review changes
* added async rest api
- Fix SQL queries - Add missing field for default project
* Pivotal ID # 174275207: Test Using The Persistence Layer - Remove persistence layer assertions - Remove deprecated methods - Remove unnecessary configuration properties
… Files (#265) * Pivotal ID # 173919045: Restrict Execute Permissions On HTTP Uploaded Files - Implement a mechanism to provide separated permissions for folders and files - Set execute permission only for folders - Improve permissions constants names - Pass down file and folder permissions independently from the files service
- Use the proper UI URL for the submission notifications - Use the application name instead of the port to kill the process - Remove unused code
* Pivotal ID # 174801815: Permissions For Deleted Submissions Add support to resubmit deleted submissions * Pivotal ID # 174801815: Permissions For Deleted Submissions Adjusts tests * code review changes Co-authored-by: Juan Camilo Rada Mesa <jcamilorada@ebi.ac.uk>
* Pivotal ID # 172671360: Warn Users About Upcoming Releases Upcoming releases RT notifications
Add the current timestamp to the submission submitted event
* added extra file fields
* Pivotal ID # 173817309: FIRE Client - Web client for the FIRE API - Add configuration properties for the FIRE service
* Pivotal #ID: 174746920: Include status fetching submissions - added subquery to ensure last version is retrieved
* Pivotal #ID 174947046: ExtSubmission list api
…x] (#288) - Validate all other possible submission statuses - Avoid calculating the MD5 every time an ExtFile is instantiated
…pendencies on SQL classes (#289) * Pivotal #ID 175632448: Extra persistence layer interfaces to avoid dependencies on SQL classes https://www.pivotaltracker.com/story/show/175632448
* Pivotal ID # 175266840: Manual Set AccNo Sequence - Generate next sequence having in mind the already existing submissions - Move concurrent processing submissions validation to the web handler level - Improve concurrent validation query - Validate the sequence exists
…pendencies on SQL classes (#290) * Pivotal #ID 175632448: Extra persistence layer interfaces to avoid dependencies on SQL classes https://www.pivotaltracker.com/story/show/175632448
- Generate next sequence having in mind the already existing submissions - Move concurrent processing submissions validation to the web handler level - Improve concurrent validation query - Validate the sequence exists
* Pivotal ID # 172671360: Warn Users About Upcoming Public Release - Add the option to filter the extended submissions based on its release time - Add operations to the web client to handle extended submissions - Implement the releaser application - Use the extended submissions to notify the upcoming releases and release the daily submissions - Create the configuration to register the releaser application - Create the daily scheduled job for the submission releaser - Create a resource to be able to trigger the releaser manually - General code improvements - Add a mechanism to enable/disable tasks in the scheduler
Add file path to the extended model
…ion tags (#296) * Pivotal #ID: 175825508: Store submission request - async processing https://www.pivotaltracker.com/story/show/175825508 * Pivotal-175839554: Include user tag as part of extended submission tags - added user tag
* Pivotal # 175163839: Submission Operations Refactor - Simplify SubmissionOperations interface and implementation - Adjust services that used these queries in order to avoid multiple DB requests - Adjust tests - Rename SimpleSubmission to BasicSubmission in order to preserve the same terms all over the code
* simplified service
- Create interface and SQL implementation for submission stats - Refactor the current code to use the new implementation - Add auto deployment in DEV environment for the master branch
Validate the submitter/owner exists when mapping an extended submission
* FTP Resource * Fixed Typos
Fix scheduler properties
Solve merge conflicts
- Fix permissions validation for a regular user resubmission - Improve the exception name and error message
Feature * Pivotal ID # 176052254: JSON Submission Attributes Validation (#310) * Pivotal #ID:175163839: Submission Query Operations In Mongo (#319) * Pivotal-176168841: Allow to check inactive user registration (#315) * Pivotal ID # 176522202: Ext Submission serialization (#322) * Pivotal ID # 172671360: Warn users about upcoming public release (#324) * Pivotal #ID 176479707: Mongo implement draft funtionality (#327) * Pivotal #ID 176479720: Mongo Metadata Query (#328) * Pivotal ID # 175163839: Mongo Submission Stats (#331) * Pivotal ID # 176886357: Async Submission Request (#334) * Pivotal ID # 176977556: Delete Submissions In Mongo (#341) * Pivotal ID #176679139: Ext Submission File List Refactor (#344) * Pivotal ID # 177042374: Delete Draft After Submission (#349) * Pivotal ID# 174948695: PTSubmit Delete Operation (#351) * Pivotal #ID 177076728: Use PMC new streaming API (#346) * Pivotal ID # 177267343: Validate EU-ToxRisk Submissions (#352) Bugfix * Pivotal ID # 176052264: Inner Folder Mapping (#311) * Pivotal ID # 172671360: Ignore Empty Value Attributes (#314) * Pivotal ID # 176377632: File list extension is missing in BIA studies (#321) * Pivotal #ID 174642598: TSV Double Quotes (#350) * Pivotal ID # 176501169: FTP Folders Missing (#335) Chore * Pivotal ID # 176377544: Add refresh users directory structure api endpoint (#320) * Pivotal #ID 176479473: Migrate biostudies test to TestContainers (#323) * Pivotal ID # 176779952: Mongo iTests CI (#332) * Pivotal #Id 176838189: Rename PMC mongo collections (#333) * Pivotal #ID: 177040448: Store request as plain json (#336) * Pivotal ID #175894089: Check if queues in RabbitMQ are persistent (#339) * Pivotal ID #177074116 : model table section properly (#338) * Pivotal ID # 176886824: Improve API Docs (#337) * Pivotal #ID 177193125: Improve collection template validation (#345) Co-authored-by: Juan <jcamilorada@ebi.ac.uk>
Juan-EBI
approved these changes
Mar 20, 2021
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