Comments (2)
Current status :
- Alembic has been integrated using the extension point
tdp-sql-database-migration
. - We have extracted the schema from the old ordino
postgres10-alpine
database and the newpostgres12.1
ordino database with the new data. - We are in the process of extracting a diff from the old and the new schema in order to update the schema on the old ordino database without deleting any data.
- Currently using a tool called pgCodeKeeper to extract the diff and compose a migration script.
- In the process of testing said script to make sure it just alters the schema without deleting any data on the target db.
from tdp_publicdb.
We discovered that a diff/upgrade from hg19 to hg38 would be too complex. That's why we will add only the missing table/columns for the hg19 to run with the newest SQL queries in Python. For now only the integration of HLA Type, MSI is considered (see Caleydo/tdp_bi_bioinfodb#63).
Add a alembic revision with the follwing content:
upgrade
- create tables
microsatelliteinstabilityview
,mutationalburden
- alter/replace the
tdp_cellline
view
- create tables
downgrade
- alter/replace the with the old
tdp_cellline
view - remove tables
microsatelliteinstabilityview
,mutationalburden
- alter/replace the with the old
Important: We only need to run this revision for hg19 and we must not run it on hg38! Manually create a table public._h19_marker
only for hg19 and check before upgrade
and downgrade
if this table exists.
Note that the table hla_a_type
(from h38) is already available as view in hg19, so no table needs to be created during the migration.
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Related Issues (20)
- Add cell line score "PRISM drug screen" HOT 1
- Unify select2 and select3 placeholder titles
- Ordino welcome tour not working
- PubMed detail view not working
- Error in GeneSymbolDetector and IDTypeDetector with non-string values
- Update requirements and dependencies
- Add Column to GeneList Tour is failing
- Remove dTiles Dependency
- Workspace does not work due to old folder in dist files
- Adding a New Single Score Column breaks the ranking HOT 2
- Domain for Boxplot Aggregated Score does not update
- Update requirements
- Update dependencies
- Update to postgres 12
- Add pgAdmin container for development purposes HOT 1
- Add json stringify to build id
- Migrate to Jest
- Make repository public
- Enable gif files
- Replace `Unkown` with missing value dash for `AA mutated`, `DNA mutated`, and `Copy Number Class`
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