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@@ -0,0 +1 @@ +/hca-util-0.2.16.tar.gz diff --git a/python-hca-util.spec b/python-hca-util.spec new file mode 100644 index 0000000..15c0d86 --- /dev/null +++ b/python-hca-util.spec @@ -0,0 +1,671 @@ +%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 <cmd> -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 <cmd> -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 <cmd> -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 +* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.16-1 +- Package Spec generated @@ -0,0 +1 @@ +7e6b267438cbe9d27bcbbc913ef95c85 hca-util-0.2.16.tar.gz |