hubmap-api-py-client 0.0.11
Client for the HuBMAP Cells API
Requires Python: >=3.8

# hubmap-api-py-client
[![PyPI version](https://badge.fury.io/py/hubmap-api-py-client.svg)](https://pypi.org/project/hubmap-api-py-client/)

Python client for the [HuBMAP Cells API](https://github.com/hubmapconsortium/cross_modality_query);
See also: [`hubmap-api-js-client`](https://github.com/hubmapconsortium/hubmap-api-js-client#readme).

Contributors start [here](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/README-contrib.md#readme).

## Usage

Install from pypi:
```
pip install hubmap-api-py-client
```

Find cells with different criteria, and intersect resulting sets:

```python
>>> from os import environ
>>> from hubmap_api_py_client import Client
>>> client = Client(environ['API_ENDPOINT'])

>>> [m for m in dir(client) if m.startswith('select_')]
['select_cells', 'select_celltypes', 'select_clusters', 'select_datasets', 'select_genes', 'select_organs', 'select_proteins']

>>> gene_symbol = client.select_genes(where="modality", has=["rna"]).get_list()[0]['gene_symbol']
>>> cells_with_gene = client.select_cells(where='gene', has=[f'{gene_symbol} > 0.5'], genomic_modality='rna')
>>> assert len(cells_with_gene) > 0

# Select cells from the datasets with the following UUIDs:
>>> dataset_a_uuid = client.select_datasets(where="gene", has=[f'{gene_symbol} > 1'], genomic_modality="rna", min_cell_percentage=0.0).get_list()[0]['uuid']
>>> dataset_b_uuid = client.select_datasets(where="gene", has=[f'{gene_symbol} > 1'], genomic_modality="rna", min_cell_percentage=0.0).get_list()[1]['uuid']
>>> cells_in_a_len = len(client.select_cells(where='dataset', has=[dataset_a_uuid]))
>>> cells_in_b_len = len(client.select_cells(where='dataset', has=[dataset_b_uuid]))
>>> cells_in_datasets = client.select_cells(where='dataset', has=[dataset_a_uuid, dataset_b_uuid])
>>> cells_in_datasets_len = len(cells_in_datasets)
>>> assert cells_in_datasets_len > 0
>>> assert cells_in_datasets_len == cells_in_a_len + cells_in_b_len

# Combine criteria with intersection:
>>> cells_with_gene_in_datasets = cells_with_gene & cells_in_datasets

# Get a list; should run quickly:
>>> cell_list = cells_with_gene.get_list()

>>> cells = cell_list[0:10]
>>> assert len(cells) > 0
>>> assert cells[0].keys() == {'cell_id', 'modality', 'dataset', 'organ', 'cell_type' ,'clusters'}

```

More documentation:
- [Examples](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/)
- [`Client` pydoc](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/README-Client.txt)
- [`ResultsSet` pydoc](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/README-external.ResultsSet.txt)
- [`ResultsList` pydoc](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/README-external.ResultsList.txt)


Only some types of objects can be retrieved from other types of objects:

| `where=...`                                                                                                             | None    | `cell`    | `cluster` | `dataset` | `gene`    | `organ`  | `protein` | `modality` | `celltype` |
|-------------------------------------------------------------------------------------------------------------------------| --------- | --------- | -------- | -------- | --------- | -------- | --------- | --------- | --------- |
| [`select_cells()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_cells.md)         | ✓         | ✓         |          | ✓        | ✓         | ✓        | ✓         | ✓         | ✓       |
| [`select_clusters()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_clusters.md)   | ✓         |           | ✓        | ✓        | ✓ ✩       | ✩        | ✩         |           | ✓       |
| [`select_datasets()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_datasets.md)   | ✓         | ✓         | ✓        | ✓        |           |✶         |           | ✓         | ✓       |
| [`select_genes()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_genes.md)         | ✓         |           | ✓ ✩      |          | ✓         | ✓ ✩      | ✩         |           |         |
| [`select_organs()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_organs.md)       | ✓         | ✓         | ✩        | ✶        | ✓ ✩       | ✓        | ✩         |           | ✓       |
| [`select_proteins()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_organs.md)     | ✓         |           | ✩        |          | ✩         | ✩        |           |           |         |
| [`select_celltypes()`](https://github.com/hubmapconsortium/hubmap-api-py-client/blob/main/examples/select_celltypes.md) | ✓         | ✓         | ✓         | ✓         | ✩         | ✓         |           |           | ✓       |


- "✓" = Supported by Cells API, and this client.
- "✶" = Supported by Entities API; support in this client is [on the roadmap](https://github.com/hubmapconsortium/hubmap-api-py-client/issues/25).
- "✩" = Possible connection to [ASCT-B](https://hubmapconsortium.github.io/ccf-asct-reporter/vis?sheet=all&dataVersion=latest) (Anatomical Structures / Cell Types / Biomarkers)