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Tools to query data from the dynamic annotation framework

Project description

# AnalysisDataLink

This repostitory will facilitate easy access to the materialized (SQL) databases once it is build up. Have a look at https://github.com/seung-lab/AnnotationPipelineOverview to get a better overview of the system.

## Accessing the SQL databases

The SQL database can be accessed in many ways, sqlAlchemy and pandas are a good place to start. Adminer is a good tool to view the database content.

### Table naming

All tables are called following a convention: ` {dataset_name}_{table_name}_v{materialization_version} ` For instance, a synapse table might be called: pinky100_pni_synapses_i3_v38.

### Pandas examples

Getting all the cell segment ids (also called root ids):

` import pandas as pd sql_query = "SELECT * FROM pinky100_cellsegment_v38" df = pd.read_sql(sql_query, database_uri, index_col="id") `

where database_uri is build as follows:

` database_uri = "postgresql://{user_name}:{password}@{database_ip}/postgres" `

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