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fastgenomics-cli-0.9.1
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FASTGenomics CLI
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fastgenomics-cli-0.9.1 |
| نام | fastgenomics-cli |
| نسخه کتابخانه | 0.9.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | FASTGenomics |
| ایمیل نویسنده | team@fastgenomics.org |
| آدرس صفحه اصلی | https://beta.fastgenomics.org |
| آدرس اینترنتی | https://pypi.org/project/fastgenomics-cli/ |
| مجوز | - |
# FASTGenomics CLI
This package is a collection of scripts to manage your data on [FASTGenomics](https://beta.fastgenomics.org).
It can be installed via
```bash
pip install fastgenomics-cli
```
and contains the following tools
## FASTGenomics Upload
This script is used to upload files via the command line.
### Usage
```bash
fg-upload [-h] [-v] [-d DATASET] [-u USER] [-p PASSWORD] [-t TITLE] [-m] [--dataset_type DATASET_TYPE] [--url URL] file [file ...]
positional arguments:
file the file(s) to be uploaded
optional arguments:
-h, --help show this help message and exit
-v, --verbose more verbose output (default: False)
-d DATASET, --dataset DATASET
add file to existing dataset with this id (default: None)
-u USER, --user USER your username (or email address) (default: None)
-p PASSWORD, --password PASSWORD
your password (default: None)
-t TITLE, --title TITLE
the title of the new dataset (default: None)
-m, --metadata upload files as metadata instead of expression data (default: False)
--dataset_type DATASET_TYPE
the dataset type (default: None)
--url URL The platform url (default: https://beta.fastgenomics.org/)
```
## FASTGenomics CLI
This script is a generic command line interface for FASTGenomics.
### Usage
```bash
fg-cli -h
```
output
```bash
usage: fg-cli [-h] {login,logout,configure-aws,version,lfs,dataset} ...
______ _____ _______ _____ _
| ____/\ / ____|__ __/ ____| (_)
| |__ / \ | (___ | | | | __ ___ _ __ ___ _ __ ___ _ ___ ___
| __/ /\ \ \___ \ | | | | |_ |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __/ __|
| | / ____ \ ____) | | | | |__| | __/ | | | (_) | | | | | | | (__\__ \
|_|/_/ \_\_____/ |_| \_____|\___|_| |_|\___/|_| |_| |_|_|\___|___/
Welcome to FASTGenomics CLI!
Version 0.12.0-c1
Here are the base commands:
optional arguments:
-h, --help show this help message and exit
FASTGenomics CLI:
{login,logout,configure-aws,version,lfs,dataset}
Actions for FASTGenomics
login Log in to the platform.
logout Log out to remove access to the platform.
configure-aws Configure AWS for the platform
version Show the version of FASTGenomics CLI.
lfs Manage Large File Storage (lfs)
dataset Manage datasets
```
### common
#### login
```bash
fg-cli login -h
```
output
```bash
usage: fg-cli login [-h] [-v] [-u USER] [-p PASSPHRASE] [-m {pat,password,bearer}] [--url URL]
Log in to the platform.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-u USER, --user USER the platform user
-p PASSPHRASE, --passphrase PASSPHRASE
the passphrase of platform user
-m {pat,password,bearer}, --login_method {pat,password,bearer}
the login method 'pat' (personal access token), 'password' or 'bearer'. Default: pat
--url URL the url of the plattform. For Example: https://beta.fastgenomics.org
```
#### logout
```bash
fg-cli logout -h
```
output
```bash
usage: fg-cli logout [-h] [-v]
Log out to remove access to the platform.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
#### version
```bash
fg-cli version -h
```
output
```bash
usage: fg-cli version [-h] [-v]
Show the version of the cli client
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
### dataset
```bash
fg-cli dataset -h
```
output
```bash
usage: fg-cli dataset [-h] {get-types,get-type-details,create,upload-file,set-metadata,delete} ...
Group: fg dataset - Manage datasets.
positional arguments:
{get-types,get-type-details,create,upload-file,set-metadata,delete}
get-types get available dataset types together with their name and description
get-type-details shows all editable fields for a dataset type
create create a dataset
upload-file upload files to dataset
set-metadata set the metadata for a dataset
delete delete a dataset
optional arguments:
-h, --help show this help message and exit
```
#### get dataset types
```bash
fg-cli dataset get-types -h
```
output
```bash
usage: fg-cli dataset get-types [-h] [-v]
get available dataset types together with their name and description
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
#### get dataset type details
```bash
fg-cli dataset get-type-details -h
```
output
```bash
usage: fg-cli dataset get-type-details [-h] [-v] [-m {brief,full}] [id]
shows all editable fields for a dataset type
positional arguments:
id the id of the dataset type
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-m {brief,full}, --mode {brief,full}
description mode. Either "full" or "brief". Default "brief".
```
#### create a dataset
```bash
fg-cli dataset create -h
```
output
```bash
usage: fg-cli dataset create [-h] [-v] [-T TITLE] [--dataset_type DATASET_TYPE]
create a dataset
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-T TITLE, --title TITLE
the title of the dataset
--dataset_type DATASET_TYPE
the dataset type. For example "cs-singlecell". To get an overview of available types use `fg-cli dataset get-types`
```
#### upload file to dataset
```bash
fg-cli dataset upload-file -h
```
output
```bash
usage: fg-cli dataset upload-file [-h] [-v] [-id ID] [-t [{primarydata,metadata}]] files [files ...]
upload files to dataset
positional arguments:
files file names of the files to be uploaded
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-id ID the id of the dataset
-t [{primarydata,metadata}], --type [{primarydata,metadata}]
the type of the file 'primaryData' or 'metaData': Default: primaryData
```
#### set metadata of a dataset
```bash
fg-cli dataset set-metadata -h
```
output
```bash
usage: fg-cli dataset set-metadata [-h] [-v] [-id ID] metadata
set the metadata for a dataset
positional arguments:
metadata the metadate to set. Use @<filename> to provide the data by file or '{ json }'. Depending on your system you might have to escape quotes accordingly.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-id ID the id of the dataset
```
set metadata by json string
```bash
fg-cli dataset set-metadata -id dataset-7463ed6a051b8557c7a03b33214e504e -d '{ "title": "new title" }'
```
set metadata by file 'meta.json' containing the json
```bash
fg-cli dataset set-metadata -id dataset-7463ed6a051b8557c7a03b33214e504e -d "@meta.json"
```
#### delete dataset
```bash
fg-cli dataset delete -h
```
output
```bash
usage: fg-cli dataset delete [-h] [-v] id
delete a dataset
positional arguments:
id the id of the dataset
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
### large file storage (lfs)
```bash
fg-cli lfs -h
```
output
```bash
usage: fg-cli lfs [-h] [-v] {create,get-url} ...
Group: fg lfs - Manage platform Large File Storage (lfs)
positional arguments:
{create,get-url}
create Create and upload a large file storage
get-url Get a download url
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
#### create lfs
```bash
fg-cli lfs create -h
```
output
```usage: fg-cli lfs create [-h] [-v] [-z [ZIP_FILENAME]] [-P [ZIP_PASSWORD]] -r RECIPIENT_EMAIL [-T [TITLE]] [--provider [{azure,aws}]] [--skip-compression] files_or_directory [files_or_directory ...]
Create and upload a large file storage
positional arguments:
files_or_directory file names or directory to be compressed
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
-z [ZIP_FILENAME], --zip-filename [ZIP_FILENAME]
name of the zip file
-P [ZIP_PASSWORD], --zip-password [ZIP_PASSWORD]
password for the zip file. if omitted a password will be generated.
-r RECIPIENT_EMAIL, --recipient-email RECIPIENT_EMAIL
the email address used in the platform of the recipient
-T [TITLE], --title [TITLE]
the title of the dataset containing the uploaded data
--provider [{azure,aws}]
the provider to be used 'azure' or 'aws'. Default: azure)
--skip-compression Skip the compression
```
#### get url of lfs
```bash
fg-cli lfs get-url -h
```
output
```bash
usage: fg-cli lfs get-url [-h] [-v] id access_token
Get a download url
positional arguments:
id the id of the storage
access_token the access token
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
#### configure AWS
```bash
fg-cli configure-aws -h
```
output
```bash
usage: fg-cli configure-aws [-h] [-v]
Configure AWS for the platform
optional arguments:
-h, --help show this help message and exit
-v, --verbose Activate verbose output
```
نیازمندی
| مقدار | نام |
|---|---|
| - | fastgenomics |
| = | requests |
| = | tqdm |
| - | update_checker |
نحوه نصب
نصب پکیج whl fastgenomics-cli-0.9.1:
pip install fastgenomics-cli-0.9.1.whl
نصب پکیج tar.gz fastgenomics-cli-0.9.1:
pip install fastgenomics-cli-0.9.1.tar.gz