Promote To BETA #474
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Promote To BETA #474
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- Validate attribute values in JSON deserialization - Fix typo
Use path for ExtFile deserialization in order to honor the inner folders
* Pivotal ID # 172671360: Ignore Empty Value Attributes - Validate empty values for attributes and attribute details in JSON deserialization - Filter out attributes and attribute details with empty values - Remove alias to improve code readability - Update schema to avoid null attribute values on the database - Remove unused code
…point (#320) Pivotal ID # 176377544: Add refresh users directory structure api endpoint Pivotal ID # 176018722: Add BioStudies client examples for external users
* added mongo support
* Pivotal-176168841: Allow to check inactive user registration https://www.pivotaltracker.com/story/show/176168841
…#321) * Pivotal ID # 176377632: File list extension is missing in BIA studies - Include the file list extension in the serialization according to the format - Include the submission folder as a source for the submission files - Remove unnecessary notification properties from the web app configuration file
* added submission serializer
* added mongo itest support
* Pivotal ID # 172671360: Warn users about upcoming public release - Log an error instead of failing when getting extended submissions - Fix notification messages
…mission is deleted https://www.pivotaltracker.com/story/show/176670057 - added logic to update modification date on the deletion
* - added interfaces for draft logic extraction * code review changes
* added project and basic submission query support
* - added access tag query support * code review changes
- added draft functionality - added projects queries
* Pivotal ID # 176779952: Mongo iTests CI - Use a Gradle property to decide whether to run the tests in Mongo or MySQL - Run both types of integration tests in the CI - Load the schema for the MySQL database container from a proper SQL script - Remove unused database column
* Pivotal ID # 175163839: Mongo Submission Stats - Implementation of the service to persist and update submission stats in Mongo - Scripts to generate a Mongo docker container for BioStudies - Add missing properties to the Submission Web App configuration - Add missing properties to the local instance configuration - Remove unnecessary step in the builder configuration - Remove unused property
* Pivotal ID # 176886357: Async Submission Request - Store files full path in Mongo documents - Adjust the files service in order to process submission files recursively and update them with the proper path - Change processing order from temp to final folder - Simplify FileService class Co-authored-by: Juan Camilo Rada Mesa <jcamilorada@ebi.ac.uk>
* Pivotal ID #177074116 : model table section properly https://www.pivotaltracker.com/story/show/177074116
* Pivotal #ID: Rename PMC mongo collections https://www.pivotaltracker.com/story/show/176838189
Fix submission deletion for mongo
* Pivotal ID # 176886824: Improve API Docs
* Pivotal ID #176679139: Ext Submission File List Refactor https://www.pivotaltracker.com/story/show/176679139
* Pivotal ID # 177042374: Delete Draft After Submission - Use interface in the resource in order to get the proper instance based on the persistence type - Remove any existing temporary draft after the submission is created - Create an endpoint to perform submissions from drafts instead of submitting page tab - Set the draft key in the submission process in order to be able to delete it once the submission is processed
* Add firemock container set-up * Add firemock container set-up for windows * Fix firemock set-up instructions Co-authored-by: Liviu Anita <liviu@ebi.ac.uk>
* Pivotal ID # 179513930: Add Warning For Empty File Lists - Change the excel reader from class to object - Use a single method to read page tab from a file - Add an exception for empty page tab files
Fix the submission url in the release message
* Pivotal ID # 179040289: BioStudies CLI Deployment Setup deployment per environment for the BioStudies CLI
* Pivotal ID # 179040289: Async Migration - Add support for async ext submissions - Include a flag in the CLI migration operation to decide whether it should be executed asynchronously - Improve log messages and remove unused code
- Improve the name of the endpoint to get the files referenced by a file list - Add support for files list located in inner folder
- Improve wording for errors related to the file lists - Remove unused constant
* Pivotal ID # 179436227: Improve Logs Messages - Adjust the submitter log messages format in order to be identified by Kibana - Include the AccNo and Submitter in each message so they can be properly indexed - Adjust tests
* Pivotal ID # 179867189: TSV Quotes Deserialization - Fix regular expression to detect values inside quotes - Add the corresponding test case
* Pivotal ID # 179939266: SpringBoot Admin App Registration - Get the process id for a specific application path - Add steps to run the integration tests in all the combinations of mongo, mysql, nfs and fire - Set the default persistence mode in the integration tests to fire
* Pivotal ID # 179922324: File Mode CLI Option - Add an option to move files instead of copying in the CLI submit operations - Adjust the involved endpoints and web client's methods - Add a converter for the "attributes" parameter
* Pivotal ID # 180152694: File List Validation Create a resource that allows validating the file lists
* Pivotal ID # 180363408: Inner Section File List Referenced Files Include inner sections for the referenced files
Improve file list validation error messages
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Feature
Pivotal ID # 177839764: FIRE FileProcessingService (#415)
Pivotal ID # 178930818: Extended File List Endpoint (#418)
Pivotal ID # 179363552: Add fire files interface source support (#436)
Pivotal ID # 178461698: FIRE Database Persistence (#437)
Pivotal ID # 179389139: FIRE Directories Persistence (#439)
Pivotal ID # 179361117: Add support for groups administration (#434)
Pivotal ID # 179609612: Submit Large Files To Fire (#444)
Pivotal ID # 179418482: Persist PageTab FIRE (#440)
Pivotal ID # 179513930: Add Warning For Empty File Lists (#448)
Pivotal ID # 179040289: Async Migration (#451)
Pivotal ID # 179810581: Files files storage (#456)
Pivotal ID # 180013760: Add submissions schema version field (#463)
Pivotal ID # 179922324: File Mode CLI Option (#465)
Pivotal ID # 180152694: File List Validation (#473)
Pivotal ID # 179921481: Fire ftp publishing (#467)
Pivotal ID # 180253535: Submission storage mode (#468)
Pivotal ID # 180282390: Reset password should activate user (#470)
Bugfix
Pivotal ID # 179145538: Handle corrupted files in PMC (#429)
Pivotal ID # 178331250: Files Names Encoding (#431)
Pivotal ID # 179435581: Deleting Submissions Isn't Working (#442)
Pivotal ID # 179904973: Fix Notification URL (#455)
Pivotal ID # 179922291: Inner File List Referenced Files (#457)
Pivotal ID # 179867189: TSV Quotes Deserialization (#462)
Pivotal ID # 180345449: handle empty title submission email notification (#472)
Chore
Pivotal ID # 179055347: Update AE user activation email (#420)
Pivotal ID # 179105055: Update Java Home (#421)
Pivotal ID # 179144369: Add tsv library (#426)
Pivotal ID # 179144780: Add json library (#427)
Pivotal ID # 179834295: Excel dsl library
Pivotal ID # 179356847: Use contanst as projects dependencies (#433)
Pivotal ID # 179355330: Simplify submission files processing (#432)
Pivotal ID # 179418565: Remove Option-Optional from backend (#438)
Pivotal ID # 179728378: On behalf register user improvements (#446)
Pivotal ID # 179436227: Improve Logs Messages (#447)
Pivotal ID # 177839916: Add firemock container set-up (#443)
Pivotal ID # 179784398: Improve all in one itest to include file list (#450)
Pivotal ID # 179040289: BioStudies CLI Deployment (#452)
Pivotal ID # 180124164: Re use ext mapping for file list (#464)
Pivotal ID # 179939266: SpringBoot Admin App Registration (#461)