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author | CoprDistGit <infra@openeuler.org> | 2023-05-05 05:41:42 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-05 05:41:42 +0000 |
commit | c10d83d9b8d93fd0a9f95db7e6ffb48a485b977b (patch) | |
tree | d737518ba357412bdb60064ca76d82375197b08d | |
parent | f7575b0fd1875879d47b36887026c73155a6c53e (diff) |
automatic import of python-ncbi-datasets-pylibopeneuler20.03
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-ncbi-datasets-pylib.spec | 360 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 362 insertions, 0 deletions
@@ -0,0 +1 @@ +/ncbi-datasets-pylib-14.26.0.tar.gz diff --git a/python-ncbi-datasets-pylib.spec b/python-ncbi-datasets-pylib.spec new file mode 100644 index 0000000..e5f465f --- /dev/null +++ b/python-ncbi-datasets-pylib.spec @@ -0,0 +1,360 @@ +%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 @@ -0,0 +1 @@ +d0a826f08523ef1d82cf458eb8d0f915 ncbi-datasets-pylib-14.26.0.tar.gz |