Remove Project Specific Code and Documentation

[joneubank]

Background

Score was originally written as software dedicated to the ICGC 25k project, and later was customized with custom implementation code for use with KidsFirst DRC. Although it has since been integrated in to the Overture DMS ecosystem, there are many vestiges of these older implementations remaining in the code base. These lingering references take many forms, from trivial code comments and naming confusion in documentation, through to dedicate packages with dedicated implementations of Score components.

At this time, it is perfectly fine to use Score as a generic product and integrate it into new projects, but the remaining project specific references in the code base can confuse Score users with:

• error messages that reference specific projects
• default configurations referencing specific environments (most of which no longer exist)
• profile names, sometimes required, that are named for specific projects and environments

Projects Referenced

• ICGC/ICGC DCC/ICGC 25K: original use case for Score from which the generic product has grown. The project portal is now retired: dcc.icgc.org
• Kids First DRC/KF: Kids First Data Resource Center
• collaboratory/collab/Cancer Collaboratory: Cloud computing platform for cancer research applications hosted until 2023 by OICR: cancercollaboratory.org

Proposed Changes

This issue is an epic used to track locations within this repo that make project specific references, and the issues created to track this work.

Issues List

• Remove ICGC References - score-fs name and type #420
• Remove ICGC References - StorageFileSystems use icgc:// scheme #421
• Remove ICGC References - Package README files #422
• Remove ICGC References - Remove comment with link to private wiki #423
• Remove ICGC References - Provide only a single Manifest Service #424
• Remove ICGC References - Rename default buckets #437
• Remove ICGC References - Remove unused scripts and static resources #438
• Remove ICGC References - Rename Custom Response Header X-ICGC-TOKEN #439
• Remove ICGC References - Remove directory score-client/integration #441
• Remove ICGC References - Rename programId in SAMFileBuilder to be "score" #442
• Remove ICGC References - Remove support email #443
• Remove ICGC References - Change error message referencing ICGC dcc #444
• Remove ICGC References - Update FUSE mount instructions #446
• Remove ICGC References - Update Error messaging in ConnectivityResponseHandler.java #447
• Remove ICGC References - Replace icgc bucketname in test files #449
• Remove KF References - Remove directory from score-client/storage/kf #458
• Remove KF References - Remove directory from score-client/resources/templates #459
• Remove KF profile from score-client/storage/ScoreStorageService #460
• Remove KF References - Remove all code referencing the profile kf #461
• Score Client Profiles - Remove program specific profiles #462
• Remove Collaboratory Reference - Rename Collaboratory StorageProfile to be S3 #463
• Score Server Profiles - Remove @Profile annotation from classes that should always be used #473
• Score Server Profiles - Introduce s3 profile to replace collaboratory, amazon, and aws #474
• Score Server Profiles - Remove hardcoded collaboratory URL in application.yaml #475

Contributing

If there are legacy project references that you discover that are not yet tracked here please open a new issue with details of the where in the repository the reference is made. Please link those issues to this one so that we can track them together.