Metadata-Version: 2.1
Name: covid-util
Version: 0.0.2
Summary: CLI tool for uploading data to the European COVID-19 data platform
Home-page: https://github.com/ebi-ait/hca-util
Author: hca-ingest-dev
Author-email: hca-ingest-dev@ebi.ac.uk
License: Apache License
Description: # covid-util
        
        CLI tool for uploading and downloading files from an HCA upload area.
        
        PyPi: https://pypi.org/project/covid-util/
        
        # 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
        Get `covid-util` from PyPi.
        
        ```shell script
        $ pip install covid-util
        ```
                                   
        ## Usage
        
        Display help
        
        ```shell script
        $ covid-util -h
        usage: covid-util [-h] [--profile PROFILE]
                           {config,create,select,dir,clear,list,upload,download,delete}
        ```
        
        In the above, optional arguments are between `[]` and choices between `{}`.
        
        The basic usage is as follows:
        
        ```shell script
        $ covid-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).
        
        ## List of commands
        
        help for a specific command:
        
        ```shell script
        $ covid-util <command> -h
        ```
        
        Some commands or options/flags are restricted to authorised users (for e.g. wranglers, admin) only.
        
        ## `config` command
        
        Configure AWS credentials
        
        ```shell script
        $ covid-util config ACCESS_KEY SECRET_KEY
        
        positional arguments:
          ACCESS_KEY         AWS Access Key ID
          SECRET_KEY         AWS Secret Access Key
        ```
        
        By default, this tool looks for and uses the profile name _covid-util_, if it exists, or it can be set by the `config` command.
        
        Running a command with the `--profile` argument uses the specified profile instead of the default _covid-util_ profile.
        
        ## `create` command
        
        Create an upload area **(authorised users only)**
        
        ```shell script
        $ covid-util create NAME [-p {u,ud,ux,udx}]
        
        
        positional arguments:
          NAME               name for the new area
        
        optional arguments:
          -n name            optional project name for new area
          -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
        
        Select or show the active upload area
        
        ```shell script
        $ covid-util select AREA
        
        positional arguments:
          AREA                area uuid. If not present then selected area is shown
        ```
        
        ## `list` command
        
        List contents of selected area
        
        ```shell script
        $ covid-util list [-b]
        
        optional arguments:
          -b                 list all areas in bucket **(authorised users only)**
        ```
        
        ## `upload` command
        
        Upload files to the selected area
        
        ```shell script
        $ covid-util upload (-a | -f file [file ...]) [-o]
        
        optional arguments:
          -a                  upload all files from current user directory
          -f file [file ...]  upload specified file(s)
          -o                  overwrite files with same names
        ```
        
        ## `download` command
        
        Download files from the selected area
        
        ```shell script
        $ covid-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
        $ covid-util delete (-a | -f file [file ...] | -d)
        
        optional arguments:
          -a                  delete all files from selected area
          -f file [file ...]  delete specified file(s) only
          -d                  delete area and contents **(authorised users only)**
        ```
        
        # Developers
        
        Run 
        
        ```shell script
        python3 -m hca_util
        ```
        
        Run tests
        
        ```shell script
        python3 -m tests.test_hca_util
        ```
        
Platform: MacOS X
Platform: Posix
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
