Generate analyses excel sheet without app running
Background
In case of ELLA downtime, we currently do not have a way of using filters, deposit configurations, usergroup configurations etc.
Implementation
We should attempt to implement this as a standalone script that can run without depending on database or a running app.
Suggest two new commands in CLI:
- Create analyses report (assuming database connection exists, and analysis has been imported)
ella-cli report analysis ANALYSIS_ID
- Should ask users to log in? Or should we provide usergroup as command line argument? Or attempt to select usergroup from analysis name/gene panel?
- Should extract current interpretation? Work log?
Attempt to create a feature rich excel workbook with sheets FILTERED ALLELES, WORKLOG(?) in addition to INFO, CLASSIFICATION, REPORT. Useful columns to use may be decided from import config, or hard coded in first iteration.
- Create analysis report (with no existing database):
make report-from-analysis
A few arguments required for this to function properly:
- Genepanels (folder?)
- usergroups.json
- filterconfigs.json
- Annotaiton config (for custom annotation, TBD)
- Usergroup to export as? Or select usergroup from name/gene panel?
- Analysis to deposit (folder, vcf, .analysis-file)
- VCF of existing classifications? (Needs a separate CLI endpoint for a not yet defined formatting)
This command should:
- Spin up a postgres server
- Create database
- Deposit gene panels
- Deposit json-files
- Deposit analysis
- Run same function as triggered by
ella-cli report analysis ANALYSIS_ID
- Clean shutdown