| Name | pyremotedata JSON |
| Version |
0.0.49
JSON |
| download |
| home_page | None |
| Summary | A package for low- and high-level high-bandwidth asynchronous data transfer |
| upload_time | 2025-07-08 10:18:50 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8.10 |
| license | None |
| keywords |
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| VCS |
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| bugtrack_url |
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No requirements were recorded.
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# `pyRemoteData`
`pyRemoteData` is a module developed for scientific computation using the remote storage platform [ERDA](https://erda.au.dk/) (Electronic Research Data Archive) provided by Aarhus University IT, as part of my PhD at the Department of Ecoscience at Aarhus University.
It can be used with **any** storage facility that supports SFTP and LFTP, but is only tested on a minimal SFTP server found at [atmoz/sftp](https://hub.docker.com/r/atmoz/sftp) and on the live AU ERDA service which runs on MiG (Minimum intrusion Grid - [SourceForge](https://sourceforge.net/projects/migrid/)/[GitHub](https://github.com/ucphhpc/migrid-sync)) developed by [SCIENCE HPC Centre at Copenhagen University](https://science.ku.dk/english/research/research-e-infrastructure/science-hpc-centre/).
## Capabilities
In order to facility high-throughput computation in a cross-platform setting, `pyRemoteData` handles data transfer with multithreading and asynchronous data streaming using thread-safe buffers.
## Use-cases
If your storage facility supports SFTP and LFTP, and you need high-bandwidth data streaming for analysis, data migration or other purposes such as model-training, then this module may be of use to you.
Experience with SFTP or LFTP is not necessary, but you must be able to setup the required SSH configurations.
See **Automated** for details on how to avoid having to set up SSH configuration.
## Setup
A more user-friendly setup process, which facilitates both automated as well as interactive setup is currently in development. (**TODO**: Finish and describe the setup process)
### Installation
The package is available on PyPI, and can be installed using pip:
```bash
pip install pyremotedata
```
### Interactive
Simply follow the popup instructions that appear once you load the package for the first time.
### Automated
The automatic configuration setup relies on setting the correct environment variables **BEFORE LOADING THE PACKAGE**:
* `PYREMOTEDATA_REMOTE_USERNAME` : Should be set to your username on your remote service.
* `PYREMOTEDATA_REMOTE_URI` : Should be set to the URI of the endpoint for your remote service (e.g. for ERDA it is "io.erda.au.dk").
* `PYREMOTEDATA_REMOTE_DIRECTORY` : If you would like to set a default working directory, that is not the root of your remote storage, then set this to that (e.g. "/MY_PROJECT/DATASETS") otherwise simply set this to "/".
* `PYREMOTEDATA_AUTO` : Should be **set to "yes"** to disable interactive mode. If this is not set, or set to anything other than "yes" (not case-sensitive), while any of the prior environment variables are unset an error will be thrown.
The recommended way to avoid any SSH or environment variables setup is to use:
```py
from pyremotedata.implicit_mount import IOHandler
with IOHandler(lftp_settings = {'sftp:connect-program' : 'ssh -a -x -i <keyfile>'}, user = <USER>, remote = <REMOTE>) as io:
...
```
Here `keyfile` is probably something like `~/.ssh/id_rsa`.
### Example
If you want to test against a mock server simply follow the instructions in tests/README.
If you have a remote storage facility that supports SFTP and LFTP, then you can use the following example to test the functionality of the module:
```python
# Set the environment variables (only necessary in a non-interactive setting)
# If you are simply running this as a Python script,
# you can omit these lines and you will be prompted to set them interactively
import os
os.environ["PYREMOTEDATA_REMOTE_USERNAME"] = "username"
os.environ["PYREMOTEDATA_REMOTE_URI"] = "storage.example.com"
os.environ["PYREMOTEDATA_REMOTE_DIRECTORY"] = "/MY_PROJECT/DATASETS"
os.environ["PYREMOTEDATA_AUTO"] = "yes"
from pyremotedata.implicit_mount import IOHandler
handler = IOHandler()
with handler as io:
print(io.ls())
# The configuration is persistent, but can be removed using the following:
from pyremotedata.config import remove_config
remove_config()
```
## Issues
This module is certainly not maximally efficient, and you may run into network- or OS-specific issues. Any and all feedback and contributions is highly appreciated.
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"description": "# `pyRemoteData`\n`pyRemoteData` is a module developed for scientific computation using the remote storage platform [ERDA](https://erda.au.dk/) (Electronic Research Data Archive) provided by Aarhus University IT, as part of my PhD at the Department of Ecoscience at Aarhus University.\n\nIt can be used with **any** storage facility that supports SFTP and LFTP, but is only tested on a minimal SFTP server found at [atmoz/sftp](https://hub.docker.com/r/atmoz/sftp) and on the live AU ERDA service which runs on MiG (Minimum intrusion Grid - [SourceForge](https://sourceforge.net/projects/migrid/)/[GitHub](https://github.com/ucphhpc/migrid-sync)) developed by [SCIENCE HPC Centre at Copenhagen University](https://science.ku.dk/english/research/research-e-infrastructure/science-hpc-centre/).\n\n## Capabilities\nIn order to facility high-throughput computation in a cross-platform setting, `pyRemoteData` handles data transfer with multithreading and asynchronous data streaming using thread-safe buffers.\n\n## Use-cases\nIf your storage facility supports SFTP and LFTP, and you need high-bandwidth data streaming for analysis, data migration or other purposes such as model-training, then this module may be of use to you.\nExperience with SFTP or LFTP is not necessary, but you must be able to setup the required SSH configurations.\n\nSee **Automated** for details on how to avoid having to set up SSH configuration.\n\n## Setup\nA more user-friendly setup process, which facilitates both automated as well as interactive setup is currently in development. (**TODO**: Finish and describe the setup process)\n\n### Installation\nThe package is available on PyPI, and can be installed using pip:\n```bash\npip install pyremotedata\n```\n\n### Interactive\nSimply follow the popup instructions that appear once you load the package for the first time.\n\n### Automated\nThe automatic configuration setup relies on setting the correct environment variables **BEFORE LOADING THE PACKAGE**:\n\n* `PYREMOTEDATA_REMOTE_USERNAME` : Should be set to your username on your remote service.\n* `PYREMOTEDATA_REMOTE_URI` : Should be set to the URI of the endpoint for your remote service (e.g. for ERDA it is \"io.erda.au.dk\").\n* `PYREMOTEDATA_REMOTE_DIRECTORY` : If you would like to set a default working directory, that is not the root of your remote storage, then set this to that (e.g. \"/MY_PROJECT/DATASETS\") otherwise simply set this to \"/\".\n* `PYREMOTEDATA_AUTO` : Should be **set to \"yes\"** to disable interactive mode. If this is not set, or set to anything other than \"yes\" (not case-sensitive), while any of the prior environment variables are unset an error will be thrown.\n\nThe recommended way to avoid any SSH or environment variables setup is to use:\n```py\nfrom pyremotedata.implicit_mount import IOHandler\nwith IOHandler(lftp_settings = {'sftp:connect-program' : 'ssh -a -x -i <keyfile>'}, user = <USER>, remote = <REMOTE>) as io:\n ...\n```\nHere `keyfile` is probably something like `~/.ssh/id_rsa`. \n\n### Example\nIf you want to test against a mock server simply follow the instructions in tests/README.\n\nIf you have a remote storage facility that supports SFTP and LFTP, then you can use the following example to test the functionality of the module:\n```python\n# Set the environment variables (only necessary in a non-interactive setting)\n# If you are simply running this as a Python script, \n# you can omit these lines and you will be prompted to set them interactively\nimport os\nos.environ[\"PYREMOTEDATA_REMOTE_USERNAME\"] = \"username\"\nos.environ[\"PYREMOTEDATA_REMOTE_URI\"] = \"storage.example.com\"\nos.environ[\"PYREMOTEDATA_REMOTE_DIRECTORY\"] = \"/MY_PROJECT/DATASETS\"\nos.environ[\"PYREMOTEDATA_AUTO\"] = \"yes\"\n\nfrom pyremotedata.implicit_mount import IOHandler\n\nhandler = IOHandler()\n\nwith handler as io:\n print(io.ls())\n\n# The configuration is persistent, but can be removed using the following:\nfrom pyremotedata.config import remove_config\nremove_config()\n```\n\n## Issues\nThis module is certainly not maximally efficient, and you may run into network- or OS-specific issues. Any and all feedback and contributions is highly appreciated.",
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