README
¶
Affix
Affix is a Medical Dataset versioning system, built in go, on IPFS, for the distributed web
Affix uses advanced language modeling and a network of scientific data engineering pipelines to produce datasets that accelerate the probability of discoveries connected to genes, proteins, pathways, RNA, molecular sequences and other biochemicals. Affix detects, extracts and validates hidden relationships between objects can quicken the pace of discovery in space biosciences.
Note that the binary is still under development and is not stable
Building From Source
To build affix you'll need the go programming language on your machine.
$ git clone https://github.com/affix-io/affix
$ cd affix
$ make install
```shell
$ affix help
and see help output.
Building on Windows
To start, make sure that you have enabled Developer Mode. A library that we depend on needs it enabled in order to properly handle symlinks. If not done, you'll likely get the error message "A required privilege is not held by the client".
You should not need to Run As Administrator to build or run affix. We do not recommend using administrator to run affix.
Shell
For your shell, we recommend using msys2. Other shells, such as cmd, Powershell, or cygwin may also be usable, but msys2 makes it easy to install our required dependencies. IPFS also recommends msys2, and affix is built on top of IPFS.
Dependencies
Building depends upon having git and make installed. If using msys2, you can easily install these by using the package manager "pacman". In a shell, type:
pacman -S git make
Assuming you've also installed go using the official Windows installer linked above, you will also need to add go to your PATH by modifying your environment variable. See the next section on "Environment variables" for more information.
Due to how msys2 treats the PATH variable, you also need to add a new environment variable MSYS2_PATH_TYPE, with the value inherit, using the same procedure.
Once these steps are complete, proceed to building.
Building on Rasberry PI
On a Raspberry PI, you'll need to increase your swap file size in order to build. Normal desktop and server linux OSes should be fine to proceed to building.
One symptom of having not enough swap space is the go install command producing an error message ending with:
link: signal: killed
To increase your swapfile size, first turn off the swapfile:
sudo dphys-swapfile swapoff
Then edit /etc/dphys-swapfile as root and set CONF_SWAPSIZE to 1024.
Finally turn on the swapfile again:
sudo dphys-swapfile swapon
Otherwise linux machines with reduced memory will have other ways to increase their swap file sizes. Check documentation for your particular machine.
Packages
affix is comprised of many specialized packages. Below you will find a summary of each package.
Documentation
¶
Overview ¶
affix is a distributed dataset version control tool. Bigger than a spreadsheet, smaller than a database, datasets are all around us. Use affix to browse, download, create, fork, and publish datasets on a peer-to-peer network that works both on and offline.
more info at: https://affix.io
Source Files
Directories
¶
| Path | Synopsis |
|---|---|
|
Package api implements a JSON-API for interacting with a affix node
|
Package api implements a JSON-API for interacting with a affix node |
|
auth
|
|
|
key/test
Package test contains predefined set of Keys for testing.
|
Package test contains predefined set of Keys for testing. |
|
Package base defines functions that operate on local data
|
Package base defines functions that operate on local data |
|
archive
Package archive creates and consumes high-fidelity conversions of dataset documents for export & import
|
Package archive creates and consumes high-fidelity conversions of dataset documents for export & import |
|
dsfs
Package dsfs glues datsets to cafs (content-addressed-file-system)
|
Package dsfs glues datsets to cafs (content-addressed-file-system) |
|
dsfs/dstest
Package dstest defines an interface for reading test cases from static files leveraging directories of test dataset input files & expected output files
|
Package dstest defines an interface for reading test cases from static files leveraging directories of test dataset input files & expected output files |
|
fill
Package fill assigns arbitrary values to struct fields using reflection.
|
Package fill assigns arbitrary values to struct fields using reflection. |
|
generate
Package generate is a command that creates a bash completion file for affix
|
Package generate is a command that creates a bash completion file for affix |