path: root/python-ncbi-datasets-pylib.spec

%global _empty_manifest_terminate_build 0
Name:		python-ncbi-datasets-pylib
Version:	14.26.0
Release:	1
Summary:	Easily gather data from across NCBI databases
License:	Public Domain
URL:		https://www.ncbi.nlm.nih.gov/datasets
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/3b/f7/8217f6cb4d2328ccd11791a19b668ad98861839d5b231f676905b086faa4/ncbi-datasets-pylib-14.26.0.tar.gz
BuildArch:	noarch


%description
[NCBI Datasets]( https://www.ncbi.nlm.nih.gov/datasets/) is a new resource that lets you easily gather data from across NCBI databases.

Find and download sequence, annotation and metadata for genes and genomes using this python library with our [RESTful API](https://www.ncbi.nlm.nih.gov/datasets/docs/datasets-api/).

This Python library is automatically generated by the [OpenAPI Generator project](https://openapi-generator.tech/).

Build package: org.openapitools.codegen.languages.PythonClientCodegen

## Requirements

Python >= 3.7

## Installation

To install the pre-built python package, create a virtual environment and use pip:

```sh
python -m venv ve/
source ve/bin/activate
pip install ncbi-datasets-pylib
```

## Getting Started

Please follow the installation procedure above and then run the following:

```python

import time
import ncbi.datasets.openapi
from pprint import pprint
from ncbi.datasets.openapi.api import gene_api
from ncbi.datasets.openapi.model.rpc_status import RpcStatus
from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary
from ncbi.datasets.openapi.model.v1_fasta import V1Fasta
from ncbi.datasets.openapi.model.v1_gene_dataset_request import V1GeneDatasetRequest
from ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type import V1GeneDatasetRequestContentType
from ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field import V1GeneDatasetRequestSortField
from ncbi.datasets.openapi.model.v1_gene_match import V1GeneMatch
from ncbi.datasets.openapi.model.v1_gene_metadata import V1GeneMetadata
from ncbi.datasets.openapi.model.v1_organism import V1Organism
from ncbi.datasets.openapi.model.v1_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter
from ncbi.datasets.openapi.model.v1_ortholog_request_content_type import V1OrthologRequestContentType
from ncbi.datasets.openapi.model.v1_ortholog_set import V1OrthologSet
from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds
from ncbi.datasets.openapi.model.v1_sort_direction import V1SortDirection
# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v1"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = 'YOUR_API_KEY'

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = gene_api.GeneApi(api_client)
    gene_ids = [
        59067,
    ] # [int] | NCBI gene ids
include_annotation_type = [
        V1Fasta("FASTA_UNSPECIFIED"),
    ] # [V1Fasta] | Select additional types of annotation to include in the data package.  If unset, no annotation is provided. (optional)
fasta_filter = [
        "fasta_filter_example",
    ] # [str] | Limit the FASTA sequences in the datasets package to these transcript and protein accessions (optional)
filename = "ncbi_dataset.zip" # str | Output file name. (optional) (default to "ncbi_dataset.zip")

    try:
        # Get a gene dataset by gene ID
        api_response = api_instance.download_gene_package(gene_ids, include_annotation_type=include_annotation_type, fasta_filter=fasta_filter, filename=filename)
        pprint(api_response)
    except ncbi.datasets.openapi.ApiException as e:
        print("Exception when calling GeneApi->download_gene_package: %s\n" % e)
```

## Documentation for API Endpoints

For detailed documentation of API endpoints, see our [GitHub page]( https://github.com/ncbi/datasets/tree/master/client_docs/python#documentation-for-api-endpoints).

## NCBI Datasets command-line tool

Alternatively, you may be interested in trying the NCBI Datasets command-line tools, datasets and dataformat.

Find out more about our command line tools in our [documentation]( https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/).


%package -n python3-ncbi-datasets-pylib
Summary:	Easily gather data from across NCBI databases
Provides:	python-ncbi-datasets-pylib
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-ncbi-datasets-pylib
[NCBI Datasets]( https://www.ncbi.nlm.nih.gov/datasets/) is a new resource that lets you easily gather data from across NCBI databases.

Find and download sequence, annotation and metadata for genes and genomes using this python library with our [RESTful API](https://www.ncbi.nlm.nih.gov/datasets/docs/datasets-api/).

This Python library is automatically generated by the [OpenAPI Generator project](https://openapi-generator.tech/).

Build package: org.openapitools.codegen.languages.PythonClientCodegen

## Requirements

Python >= 3.7

## Installation

To install the pre-built python package, create a virtual environment and use pip:

```sh
python -m venv ve/
source ve/bin/activate
pip install ncbi-datasets-pylib
```

## Getting Started

Please follow the installation procedure above and then run the following:

```python

import time
import ncbi.datasets.openapi
from pprint import pprint
from ncbi.datasets.openapi.api import gene_api
from ncbi.datasets.openapi.model.rpc_status import RpcStatus
from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary
from ncbi.datasets.openapi.model.v1_fasta import V1Fasta
from ncbi.datasets.openapi.model.v1_gene_dataset_request import V1GeneDatasetRequest
from ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type import V1GeneDatasetRequestContentType
from ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field import V1GeneDatasetRequestSortField
from ncbi.datasets.openapi.model.v1_gene_match import V1GeneMatch
from ncbi.datasets.openapi.model.v1_gene_metadata import V1GeneMetadata
from ncbi.datasets.openapi.model.v1_organism import V1Organism
from ncbi.datasets.openapi.model.v1_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter
from ncbi.datasets.openapi.model.v1_ortholog_request_content_type import V1OrthologRequestContentType
from ncbi.datasets.openapi.model.v1_ortholog_set import V1OrthologSet
from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds
from ncbi.datasets.openapi.model.v1_sort_direction import V1SortDirection
# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v1"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = 'YOUR_API_KEY'

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = gene_api.GeneApi(api_client)
    gene_ids = [
        59067,
    ] # [int] | NCBI gene ids
include_annotation_type = [
        V1Fasta("FASTA_UNSPECIFIED"),
    ] # [V1Fasta] | Select additional types of annotation to include in the data package.  If unset, no annotation is provided. (optional)
fasta_filter = [
        "fasta_filter_example",
    ] # [str] | Limit the FASTA sequences in the datasets package to these transcript and protein accessions (optional)
filename = "ncbi_dataset.zip" # str | Output file name. (optional) (default to "ncbi_dataset.zip")

    try:
        # Get a gene dataset by gene ID
        api_response = api_instance.download_gene_package(gene_ids, include_annotation_type=include_annotation_type, fasta_filter=fasta_filter, filename=filename)
        pprint(api_response)
    except ncbi.datasets.openapi.ApiException as e:
        print("Exception when calling GeneApi->download_gene_package: %s\n" % e)
```

## Documentation for API Endpoints

For detailed documentation of API endpoints, see our [GitHub page]( https://github.com/ncbi/datasets/tree/master/client_docs/python#documentation-for-api-endpoints).

## NCBI Datasets command-line tool

Alternatively, you may be interested in trying the NCBI Datasets command-line tools, datasets and dataformat.

Find out more about our command line tools in our [documentation]( https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/).


%package help
Summary:	Development documents and examples for ncbi-datasets-pylib
Provides:	python3-ncbi-datasets-pylib-doc
%description help
[NCBI Datasets]( https://www.ncbi.nlm.nih.gov/datasets/) is a new resource that lets you easily gather data from across NCBI databases.

Find and download sequence, annotation and metadata for genes and genomes using this python library with our [RESTful API](https://www.ncbi.nlm.nih.gov/datasets/docs/datasets-api/).

This Python library is automatically generated by the [OpenAPI Generator project](https://openapi-generator.tech/).

Build package: org.openapitools.codegen.languages.PythonClientCodegen

## Requirements

Python >= 3.7

## Installation

To install the pre-built python package, create a virtual environment and use pip:

```sh
python -m venv ve/
source ve/bin/activate
pip install ncbi-datasets-pylib
```

## Getting Started

Please follow the installation procedure above and then run the following:

```python

import time
import ncbi.datasets.openapi
from pprint import pprint
from ncbi.datasets.openapi.api import gene_api
from ncbi.datasets.openapi.model.rpc_status import RpcStatus
from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary
from ncbi.datasets.openapi.model.v1_fasta import V1Fasta
from ncbi.datasets.openapi.model.v1_gene_dataset_request import V1GeneDatasetRequest
from ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type import V1GeneDatasetRequestContentType
from ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field import V1GeneDatasetRequestSortField
from ncbi.datasets.openapi.model.v1_gene_match import V1GeneMatch
from ncbi.datasets.openapi.model.v1_gene_metadata import V1GeneMetadata
from ncbi.datasets.openapi.model.v1_organism import V1Organism
from ncbi.datasets.openapi.model.v1_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter
from ncbi.datasets.openapi.model.v1_ortholog_request_content_type import V1OrthologRequestContentType
from ncbi.datasets.openapi.model.v1_ortholog_set import V1OrthologSet
from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds
from ncbi.datasets.openapi.model.v1_sort_direction import V1SortDirection
# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v1"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = 'YOUR_API_KEY'

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = gene_api.GeneApi(api_client)
    gene_ids = [
        59067,
    ] # [int] | NCBI gene ids
include_annotation_type = [
        V1Fasta("FASTA_UNSPECIFIED"),
    ] # [V1Fasta] | Select additional types of annotation to include in the data package.  If unset, no annotation is provided. (optional)
fasta_filter = [
        "fasta_filter_example",
    ] # [str] | Limit the FASTA sequences in the datasets package to these transcript and protein accessions (optional)
filename = "ncbi_dataset.zip" # str | Output file name. (optional) (default to "ncbi_dataset.zip")

    try:
        # Get a gene dataset by gene ID
        api_response = api_instance.download_gene_package(gene_ids, include_annotation_type=include_annotation_type, fasta_filter=fasta_filter, filename=filename)
        pprint(api_response)
    except ncbi.datasets.openapi.ApiException as e:
        print("Exception when calling GeneApi->download_gene_package: %s\n" % e)
```

## Documentation for API Endpoints

For detailed documentation of API endpoints, see our [GitHub page]( https://github.com/ncbi/datasets/tree/master/client_docs/python#documentation-for-api-endpoints).

## NCBI Datasets command-line tool

Alternatively, you may be interested in trying the NCBI Datasets command-line tools, datasets and dataformat.

Find out more about our command line tools in our [documentation]( https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/).


%prep
%autosetup -n ncbi-datasets-pylib-14.26.0

%build
%py3_build

%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .

%files -n python3-ncbi-datasets-pylib -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 14.26.0-1
- Package Spec generated