To help you get started, we've collected the most common ways that solvebio is being used within popular public projects.

chop-dbhi / varify / varify / variants / resources.py View on Github

# this variant then there is no benefit to including it.
            samples_with_variant = cv.cohort.samples.filter(
                results__variant=cv.variant)

            cohort_data['samples'] = serialize(samples_with_variant,
                                               **api.templates.SimpleSample)

            cohort_list.append(cohort_data)

        data['cohorts'] = cohort_list

        if SolveBio and SolveBio.is_enabled():
            data['solvebio'] = {}

            # ClinVar integration -- use position and HGVS
            filters = Filter(chromosome=variant.chr.value,
                             start__lte=variant.pos,
                             stop__gte=variant.pos)

            if hgvs_c_values:
                filters = filters | Filter(hgvs_c__in=list(hgvs_c_values))

            # TODO: add another clinvar query for reported gene-wide variants
            # if genes:
            #     filters = filters | Filter(gene_symbol__in=list(genes))

            try:
                # Query ClinVar by its alias, return 10 results/page
                # TODO: client-side pagination
                q = SolveBio.get_dataset('clinvar').query(
                    limit=10,  # limit to 10 results (single page)
                    filters=filters)

View more ways to use solvebio

SolveBio Python Client

This is the SolveBio Python package and command-line interface (CLI). This module is tested against Python 2.7, 3.6, 3.7, 3.8, 3.10, PyPy and PyPy3.

Developer documentation is available at docs.solvebio.com. For more information about SolveBio visit www.solvebio.com.

Installation & Setup

Install solvebio using pip:

pip install solvebio

For interactive use, we recommend installing IPython and gnureadline:

pip install ipython
pip install gnureadline

To log in, type:

solvebio login

Enter your SolveBio credentials and you should be good to go!

Install from Git

pip install -e git+https://github.com/solvebio/solvebio-python.git#egg=solve

Development

git clone https://github.com/solvebio/solvebio-python.git
cd solve-python/
python setup.py develop

Or install tox and run:

pip install tox
tox

Releasing

You will need to configure Twine in order to push to PyPI.

Maintainers can release solvebio-python to PyPI with the following steps:

bumpversion 
git push --tags
make changelog
make release

Support

Developer documentation is available at docs.solvebio.com.

If you experience problems with this package, please create a GitHub Issue.

For all other requests, please email SolveBio Support.

Configuring the Client

The SolveBio python client can be configured by setting system environment variables. Supported environment variables are:

SOLVEBIO_API_HOST

• The URL of the target API backend. If not specified the value from the local credentials file will be used.

SOLVEBIO_ACCESS_TOKEN

• The OAuth2 access token for authenticating with the API.

SOLVEBIO_API_KEY

• The API Key to use for authenticating with the API.

The lookup order for credentials is:

1. Access Token
2. API Key
3. Local Credentials file

SOLVEBIO_LOGLEVEL

• The log level at which to log messages. If not specified the default log level will be WARN.

SOLVEBIO_LOGFILE

• The file in which to write log messages. If the file does not exist it will be created. If not specified '~/.solvebio/solvebio.log' will be used by default.

SOLVEBIO_RETRY_ALL

• Flag for enabling aggressive retries for failed requests to the API. When truthy, the client will attempt to retry a failed request regardless of the type of operation. This includes idempotent and nonidempotent operations: "HEAD", "GET", "PUT", "POST", "PATCH", "DELETE", "OPTIONS", "TRACE" If this value is not set it will default to false and retries will only be enabled for idempotent operations.