%global _empty_manifest_terminate_build 0 Name: python-hca-util Version: 0.2.16 Release: 1 Summary: CLI tool for uploading data to the HCA data platform License: Apache License URL: https://github.com/ebi-ait/hca-util Source0: https://mirrors.nju.edu.cn/pypi/web/packages/d2/d9/d6761138a424572b78d0401e197ee74dd9fda735619e1db6d96c460ed172/hca-util-0.2.16.tar.gz BuildArch: noarch Requires: python3-boto3 Requires: python3-botocore Requires: python3-filetype Requires: python3-requests Requires: python3-tqdm %description # hca-util CLI tool for uploading data to the Human Cell Atlas AWS S3 buckets. # Users ## Prerequisites Users need to have 1. Basic command-line knowledge 2. Python3.x installed on their machine 3. Credentials to access data in the S3 bucket (access and secret keys) ## Install The [hca-util](https://pypi.org/project/hca-util/) tool is available to install from PyPi. ```shell script $ pip install hca-util ``` Note there is a version of this tool published as [covid-util](https://pypi.org/project/covid-util/) in PyPi for uploading data to the European COVID-19 data platform. This version uses its own separate data storage and access credentials. ## Usage Display help and list of commands. ```shell script $ hca-util -h usage: hca-util [-h] [--version] [--profile PROFILE] {config,create,select,list,upload,download,delete} ... hca-util optional arguments: -h, --help show this help message and exit --version, -v show program's version number and exit --profile PROFILE use PROFILE instead of default 'hca-util' profile command: {config,create,select,list,upload,download,delete} config configure AWS credentials create create an upload area (authorised users only) select select or show the active upload area list list contents of the area upload upload files to the area download download files from the area delete delete files from the area ``` In the above, optional arguments are between `[]` and choices between `{}`. The basic usage is as follows: ```shell script $ hca-util cmd ARG1 ARG2 -o1 -o2 ``` Use the tool by specifying a command (`cmd` - see list below) to run, any mandatory (positional) arguments (e.g. `ARG1` and `ARG2` - see positional args for each command), and any optional arguments (e.g. `-o1` and `o2` - see options for each command). ## Commands Help with specific command: ```shell script $ hca-util -h ``` Some commands or options/flags are restricted to authorised users (admin) only. ## `config` command Configure AWS credentials ```shell script $ hca-util config ACCESS_KEY SECRET_KEY positional arguments: ACCESS_KEY AWS Access Key ID SECRET_KEY AWS Secret Access Key ``` The tool uses the profile name _hca-util_ in local AWS config files. Once configured, the set up can be checked by running the command again, this time without credentials (`hca-util config`), to verify if the previously entered credentials are valid or not. ## `create` command Create an upload area **(authorised users only)** ```shell script $ hca-util create NAME [-p {u,ud,ux,udx}] positional arguments: NAME name for the new area optional arguments: -p {u,ud,ux,udx} allowed actions (permissions) on new area. u for upload, x for delete and d for download. Default is ux ``` ## `select` command Show or select the active upload area ```shell script $ hca-util select AREA positional arguments: AREA area uuid. ``` If AREA is not specified, the selected area is shown. ## `list` command List contents of selected area ```shell script $ hca-util list [-b] optional arguments: -b list all areas in bucket **(authorised users only)** ``` ## `upload` command Upload files to the selected area ```shell script $ hca-util upload PATH [PATH ...] [-o] positional arguments: PATH valid file or directory optional arguments: -o overwrite files with same names ``` ## `download` command Download files from the selected area ```shell script $ hca-util download (-a | -f file [file ...]) optional arguments: -a download all files from selected area -f file [file ...] download specified file(s) only ``` ## `delete` command Delete files from the selected area ```shell script $ hca-util delete [-a | -d] [PATH [PATH ...]] positional arguments: PATH path to file or directory to delete optional arguments: -a delete all files from the area -d delete upload area and contents (authorised users only) ``` ## `sync` command Transfer files from the selected area to Ingest upload area ```shell script $ hca-util sync INGEST_UPLOAD_AREA positional arguments: INGEST_UPLOAD_AREA Ingest upload area ``` INGEST_UPLOAD_AREA format: `s3://org-hca-data-archive-upload-_ENV_/_UUID_/` # Developers Download dependencies ``` pip install -r requirements.txt ``` Run ```shell script python3 -m ait.commons.util ``` Run tests ```shell script nosetests ``` %package -n python3-hca-util Summary: CLI tool for uploading data to the HCA data platform Provides: python-hca-util BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-hca-util # hca-util CLI tool for uploading data to the Human Cell Atlas AWS S3 buckets. # Users ## Prerequisites Users need to have 1. Basic command-line knowledge 2. Python3.x installed on their machine 3. Credentials to access data in the S3 bucket (access and secret keys) ## Install The [hca-util](https://pypi.org/project/hca-util/) tool is available to install from PyPi. ```shell script $ pip install hca-util ``` Note there is a version of this tool published as [covid-util](https://pypi.org/project/covid-util/) in PyPi for uploading data to the European COVID-19 data platform. This version uses its own separate data storage and access credentials. ## Usage Display help and list of commands. ```shell script $ hca-util -h usage: hca-util [-h] [--version] [--profile PROFILE] {config,create,select,list,upload,download,delete} ... hca-util optional arguments: -h, --help show this help message and exit --version, -v show program's version number and exit --profile PROFILE use PROFILE instead of default 'hca-util' profile command: {config,create,select,list,upload,download,delete} config configure AWS credentials create create an upload area (authorised users only) select select or show the active upload area list list contents of the area upload upload files to the area download download files from the area delete delete files from the area ``` In the above, optional arguments are between `[]` and choices between `{}`. The basic usage is as follows: ```shell script $ hca-util cmd ARG1 ARG2 -o1 -o2 ``` Use the tool by specifying a command (`cmd` - see list below) to run, any mandatory (positional) arguments (e.g. `ARG1` and `ARG2` - see positional args for each command), and any optional arguments (e.g. `-o1` and `o2` - see options for each command). ## Commands Help with specific command: ```shell script $ hca-util -h ``` Some commands or options/flags are restricted to authorised users (admin) only. ## `config` command Configure AWS credentials ```shell script $ hca-util config ACCESS_KEY SECRET_KEY positional arguments: ACCESS_KEY AWS Access Key ID SECRET_KEY AWS Secret Access Key ``` The tool uses the profile name _hca-util_ in local AWS config files. Once configured, the set up can be checked by running the command again, this time without credentials (`hca-util config`), to verify if the previously entered credentials are valid or not. ## `create` command Create an upload area **(authorised users only)** ```shell script $ hca-util create NAME [-p {u,ud,ux,udx}] positional arguments: NAME name for the new area optional arguments: -p {u,ud,ux,udx} allowed actions (permissions) on new area. u for upload, x for delete and d for download. Default is ux ``` ## `select` command Show or select the active upload area ```shell script $ hca-util select AREA positional arguments: AREA area uuid. ``` If AREA is not specified, the selected area is shown. ## `list` command List contents of selected area ```shell script $ hca-util list [-b] optional arguments: -b list all areas in bucket **(authorised users only)** ``` ## `upload` command Upload files to the selected area ```shell script $ hca-util upload PATH [PATH ...] [-o] positional arguments: PATH valid file or directory optional arguments: -o overwrite files with same names ``` ## `download` command Download files from the selected area ```shell script $ hca-util download (-a | -f file [file ...]) optional arguments: -a download all files from selected area -f file [file ...] download specified file(s) only ``` ## `delete` command Delete files from the selected area ```shell script $ hca-util delete [-a | -d] [PATH [PATH ...]] positional arguments: PATH path to file or directory to delete optional arguments: -a delete all files from the area -d delete upload area and contents (authorised users only) ``` ## `sync` command Transfer files from the selected area to Ingest upload area ```shell script $ hca-util sync INGEST_UPLOAD_AREA positional arguments: INGEST_UPLOAD_AREA Ingest upload area ``` INGEST_UPLOAD_AREA format: `s3://org-hca-data-archive-upload-_ENV_/_UUID_/` # Developers Download dependencies ``` pip install -r requirements.txt ``` Run ```shell script python3 -m ait.commons.util ``` Run tests ```shell script nosetests ``` %package help Summary: Development documents and examples for hca-util Provides: python3-hca-util-doc %description help # hca-util CLI tool for uploading data to the Human Cell Atlas AWS S3 buckets. # Users ## Prerequisites Users need to have 1. Basic command-line knowledge 2. Python3.x installed on their machine 3. Credentials to access data in the S3 bucket (access and secret keys) ## Install The [hca-util](https://pypi.org/project/hca-util/) tool is available to install from PyPi. ```shell script $ pip install hca-util ``` Note there is a version of this tool published as [covid-util](https://pypi.org/project/covid-util/) in PyPi for uploading data to the European COVID-19 data platform. This version uses its own separate data storage and access credentials. ## Usage Display help and list of commands. ```shell script $ hca-util -h usage: hca-util [-h] [--version] [--profile PROFILE] {config,create,select,list,upload,download,delete} ... hca-util optional arguments: -h, --help show this help message and exit --version, -v show program's version number and exit --profile PROFILE use PROFILE instead of default 'hca-util' profile command: {config,create,select,list,upload,download,delete} config configure AWS credentials create create an upload area (authorised users only) select select or show the active upload area list list contents of the area upload upload files to the area download download files from the area delete delete files from the area ``` In the above, optional arguments are between `[]` and choices between `{}`. The basic usage is as follows: ```shell script $ hca-util cmd ARG1 ARG2 -o1 -o2 ``` Use the tool by specifying a command (`cmd` - see list below) to run, any mandatory (positional) arguments (e.g. `ARG1` and `ARG2` - see positional args for each command), and any optional arguments (e.g. `-o1` and `o2` - see options for each command). ## Commands Help with specific command: ```shell script $ hca-util -h ``` Some commands or options/flags are restricted to authorised users (admin) only. ## `config` command Configure AWS credentials ```shell script $ hca-util config ACCESS_KEY SECRET_KEY positional arguments: ACCESS_KEY AWS Access Key ID SECRET_KEY AWS Secret Access Key ``` The tool uses the profile name _hca-util_ in local AWS config files. Once configured, the set up can be checked by running the command again, this time without credentials (`hca-util config`), to verify if the previously entered credentials are valid or not. ## `create` command Create an upload area **(authorised users only)** ```shell script $ hca-util create NAME [-p {u,ud,ux,udx}] positional arguments: NAME name for the new area optional arguments: -p {u,ud,ux,udx} allowed actions (permissions) on new area. u for upload, x for delete and d for download. Default is ux ``` ## `select` command Show or select the active upload area ```shell script $ hca-util select AREA positional arguments: AREA area uuid. ``` If AREA is not specified, the selected area is shown. ## `list` command List contents of selected area ```shell script $ hca-util list [-b] optional arguments: -b list all areas in bucket **(authorised users only)** ``` ## `upload` command Upload files to the selected area ```shell script $ hca-util upload PATH [PATH ...] [-o] positional arguments: PATH valid file or directory optional arguments: -o overwrite files with same names ``` ## `download` command Download files from the selected area ```shell script $ hca-util download (-a | -f file [file ...]) optional arguments: -a download all files from selected area -f file [file ...] download specified file(s) only ``` ## `delete` command Delete files from the selected area ```shell script $ hca-util delete [-a | -d] [PATH [PATH ...]] positional arguments: PATH path to file or directory to delete optional arguments: -a delete all files from the area -d delete upload area and contents (authorised users only) ``` ## `sync` command Transfer files from the selected area to Ingest upload area ```shell script $ hca-util sync INGEST_UPLOAD_AREA positional arguments: INGEST_UPLOAD_AREA Ingest upload area ``` INGEST_UPLOAD_AREA format: `s3://org-hca-data-archive-upload-_ENV_/_UUID_/` # Developers Download dependencies ``` pip install -r requirements.txt ``` Run ```shell script python3 -m ait.commons.util ``` Run tests ```shell script nosetests ``` %prep %autosetup -n hca-util-0.2.16 %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-hca-util -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Tue May 30 2023 Python_Bot - 0.2.16-1 - Package Spec generated