Clinical-Genomics / cg / 9870472988

86%

Build Type

push

github

Committed by web-flow

Commit Message

Re-route flow to illumina device tables. (#3349)(major)

# Description

Feature branch to re-route the post-processing database flow from the `Flowcell` -> `SampleLaneSequencingMetrics` model paradigm to `IlluminaFlowCell` -> `IlluminaSequencingRun` -> `IlluminaSampleSequencingMetrics`. 
The choice to use a feature branch is to collect all changes and make sure they are tested. Since we need to alter core logic that requires a database migration we cannot do these step by step.

PR in servers: https://github.com/Clinical-Genomics/servers/pull/1394
Data migration script: https://github.com/Clinical-Genomics/add-new-tech/issues/7

## Deploy
```shell
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b develop-illumina-devices -a
```

## CLI command changes
Commands that need to be updated in servers

- [x] `cg clean flow-cells` -> `cg clean illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup encrypt-flow-cells` -> `cg backup encrypt-illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup flow-cells` -> `cg backup illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup fetch-flow-cell`-> `cg backup fetch-illumina-run` (no update needed)
- [x] `cg demultiplex finish flow-cell` -> `cg demultiplex finish illumina-run` (no update needed in servers
- [x] `cg get flow-cell` -> `cg get sequencing-run` (Does not require a PR in servers)
- [x] `cg set flowcell` -> `cg set sequencing-run` (Does not require a PR in servers)
- [x] `cg store flow-cell`-> `cg store illumina-run` (Does not require a PR in servers)
- [x] `cg store demultiplexed-flow-cell` -> `cg store demultiplexed-run` (Does not require a PR in servers)
- [x] `cg decompress flow-cell` -> `cg decompress illumina-run` (Does not require a PR in servers)

Run Details

732 of 848 new or added lines in 58 files covered. (86.32%)

23 existing lines in 11 files now uncovered.

20432 of 24239 relevant lines covered (84.29%)

0.84 hits per line