[docs] Writing data manually to a var SOMA DataFrame causes TileDB internal error

[mdylan2]

Describe the bug
Trying to write some data to a var dataframe but I hit the following error:

TileDB internal: ['UnorderedWriter::dowork]  (FragmentMetadata: Cells are written outside of the defined current domain.)

What am I doing wrong?

To Reproduce

import pandas as pd
import pyarrow as pa
import tiledbsoma as soma
import os
import shutil

EXP_URI = "test"
try:
    # Step 1: Create a simple dataframe with three columns
    data = {
        'gene': ['GeneA', 'GeneB', 'GeneC', 'GeneD', 'GeneE'],
        'ens': ['ENSG0001', 'ENSG0002', 'ENSG0003', 'ENSG0004', 'ENSG0005'],
        'soma_joinid': [1, 2, 3, 4, 5]
    }

    df = pd.DataFrame(data)

    # Step 2: Initialize the soma.Experiment and collections
    exp = soma.Experiment.create(EXP_URI)
    ms = exp.add_new_collection('ms')
    rna = ms.add_new_collection('RNA', soma.Measurement)

    # Step 3: Define the schema
    schema = {
        "soma_joinid": pa.int64(),
        "gene": pa.large_string(),
        "ens": pa.large_string()
    }

    # Step 5: Define the schema for the dataframe
    var_schema = pa.schema(list(schema.items()))

    # Step 6: Create the dataframe in the rna collection
    var = rna.add_new_dataframe("var", schema=var_schema, index_column_names=["soma_joinid"])

    # Step 7: Write the pandas dataframe to the soma dataframe
    var.write(pa.Table.from_pandas(df))
    print("SUCCESS!")
    
except Exception as e:
    rna.close()
    ms.close()
    exp.close()
    print("--> EXCEPTION")
    print("Exception hit:", e)
    if os.path.exists(EXP_URI):
        shutil.rmtree(EXP_URI)

Versions (please complete the following information):

• TileDB-SOMA version: 1.15.2
• Tiledb version: 0.33.2
• Language and language version (e.g. Python 3.9, R 4.3.2): 3.12.3
• OS (e.g. MacOS, Ubuntu Linux): Ubuntu
• Note: you can use tiledbsoma.show_package_versions() (Python) or tiledbsoma::show_package_versions() (R)

Additional context
Add any other context about the problem here.

[johnkerl]

Hi @mdylan2 ! Please check out this doc page:

https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/shapes/

[johnkerl]

Specficially, you need domain here:

    var = rna.add_new_dataframe("var", schema=var_schema, index_column_names=["soma_joinid"])

[johnkerl]

Since soma_joinid nominally starts at 0 (although this isn't required) you could do either

    var = rna.add_new_dataframe("var", schema=var_schema, domain=[[1,5]], index_column_names=["soma_joinid"])

or

    var = rna.add_new_dataframe("var", schema=var_schema, domain=[[0,5]], index_column_names=["soma_joinid"])