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Update to v2.0.0 #70

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Oct 13, 2023
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Update to v2.0.0 #70

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23 changes: 21 additions & 2 deletions README.md
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# Single Cell Expression Atlas database loading module (v1.0.0)
# Single Cell Expression Atlas database loading module (v2.0.0)

A [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc) module for loading experiments to a Postgres 11
database. Release v0.4.0 was used for [the October 2022 data release of Single Cell Expression
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delete_db_scxa_dimred.sh
```

## `scxa_cell_group` and `scxa_cell_group_membership` table
## `scxa_cell_group` and `scxa_cell_group_membership` tables

### Load data
Run `bin/load_db_scxa_cell_clusters.sh`. It requires the following environment variables:
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delete_db_scxa_marker_genes.sh
```

## `exp_design` and `exp_design_column` tables

### Load data
Run `bin/load_exp_design.sh`. It requires the following environment variables:

| Variable name | Description |
|-----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `CONDENSED_SDRF_FILE` | Path of the condensed SDRF file of the experiment being loaded |
| `SDRF_FILE` | Path of the SDRF file of the experiment being loaded |
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| `dbConnection` | A Postgres connection string in the form `postgresql://{user}:{password}@{host:port}/{databaseName}` pointing to a Postgres 11 server where the expected `scxa_cell_group_marker_genes` and `scxa_cell_group_marker_gene_stats` tables exist |

### Delete data
Currently, there’s no script to delete data from these tables. You can do it manually with the following SQL statements:

```sql
DELETE FROM exp_design WHERE exp_design_column_id IN (SELECT id FROM exp_design_column WHERE experiment_accession='E-FOO-123');
DELETE FROM exp_design_column WHERE experiment_accession='E-FOO-123';
```

## Post-loading a batch of experiments
Once a number of experiments have been loaded, tables should be re-indexed:

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