• https://raw.githubusercontent.com/oeg-upm/ya2ro/main/Dockerfile

Description

Active: The project has reached a stable, usable state and is being actively developed.

More information

https://www.repostatus.org/#active:

To run ya2ro, please follow the next steps:

pip install ya2ro

git clone https://github.com/oeg-upm/ya2ro
cd ya2ro
pip install -e .

We provide a Dockerfile with ya2ro already installed. To run through Docker, you may build the Dockerfile provided in the repository by running:

docker build -t ya2ro .

Then, to run your image just type:

docker run -it ya2ro /bin/bash

And you will be ready to use ya2ro (see section below). If you want to have access to the results we recommend mounting a volume. For example, the following command will mount the current directory as the out folder in the Docker image:

docker run -it --rm -v $PWD/:/out ya2ro /bin/bash

If you move any files produced by ya2ro into /out, then you will be able to see them in your current directory.

ya2ro --help

If everything goes fine, you should see:

                        ad888888b,
                       d8"     "88
                               a8P
8b       d8 ,adPPYYba,      ,d8P"  8b,dPPYba,  ,adPPYba,
`8b     d8' ""     `Y8    a8P"     88P'   "Y8 a8"     "8a
 `8b   d8'  ,adPPPPP88  a8P'       88         8b       d8
  `8b,d8'   88,    ,88 d8"         88         "8a,   ,a8"
    Y88'    `"8bbdP"Y8 88888888888 88          `"YbbdP"'
    d8'
   d8'
_________________________________________________________

usage: ya2ro [-h] (-i YAML_PATH | -l YA2RO_PREV_OUTPUT) [-o OUTPUT_DIR] [-p PROPERTIES_FILE] [-ns]

Human and machine readable input as a yaml file and create RO-Object in jsonld and/or HTML view. Run 'ya2ro -configure GITHUB_PERSONAL_ACCESS_TOKEN' this the first time to configure ya2ro
properly

options:
  -h, --help            show this help message and exit
  -i YAML_PATH, --input YAML_PATH
                        Path of the required yaml input. Follow the documentation or the example given to see the structure of the file.
  -l YA2RO_PREV_OUTPUT, --landing_page YA2RO_PREV_OUTPUT
                        Path of a previous output folder using the ya2ro tool. This flag will make a landing page to make all the resources accessible.
  -o OUTPUT_DIR, --output_directory OUTPUT_DIR
                        Output directory.
  -p PROPERTIES_FILE, --properties_file PROPERTIES_FILE
                        Properties file name.
  -ns, --no_somef       Disable SOMEF for a faster execution (software cards will not work).

https://oeg-upm.github.io/ya2ro/output/landing_page.html

Before running ya2ro, you must configure it appropriately. Please add your personal token in ya2ro properties file.
--> ~/ya2ro/src/ya2ro/resources/properties.yaml <--

Add a line like the following:

# Add here your GitHub personal access token
GITHUB_PERSONAL_ACCESS_TOKEN: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

ya2ro will continue working if not configured, but is highly recommended to apply this setting.

The first thing to do is create some input for ya2ro. To create valid a yaml you should follow the documentation bellow.

Create a yaml from scratch or use one of the supplied templates. Currently ya2ro supports two formats:

• paper
• project

Please find a template for each type under the directory templates. Once you have a valid yaml (project or paper) is time to run ya2ro.

It is possible to process batches of yamls at the same time, to do that just specify as input a folder with all the yamls inside.

ya2ro -i templates

ya2ro -i templates/project_template.yaml

ya2ro -input templates --output_directory out --properties_file custom_properties.yaml

ya2ro -i templates -o out -p custom_properties.yaml

Use the flag --no_somef or -ns for disabling SOMEF which is the most time consuming process.

ya2ro -i templates -ns

WARNING: Software cards will no longer work on github links. Therefore you will need to manually insert the software data in the yaml file.

ya2ro offers the option to create a landing page where all the resources produced are easily accessible. Just indicate the folder where this resources are, for example:

ya2ro -l output

• https://mybinder.org/v2/gh/KnowledgeCaptureAndDiscovery/somef/HEAD?filepath=notebook%2FSOMEF%20Usage%20Example.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/experiments/TFidf-NB.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/experiments/TFidf-Logistic.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/experiments/Classifier%20Pipelines.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/experiments/initial_baseline.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/experiments/header_analysis/Wordnet.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/notebook/SOMEF%20Usage%20Example.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/02-kg-profiling.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/05-kg-enrichment-with-lod.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/06-kg-network-analysis.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/kgtk-browser.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/03-kg-graph-embeddings.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/04-kg-enrichment-with-csv.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/07-kg-constraint-validation.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/tutorial/01-kgtk-introduction.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/use-cases/browser-profiling.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/use-cases/class-visualization.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/use-cases/ontology-examples.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/use-cases/properties-for-this-type.ipynb
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/kgtk-notebooks/use-cases/Visualize-force-graph-example.ipynb

• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/src/somef/test/test_data/repositories/wot-hive/docker/docker-compose.yml
• https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/master/Dockerfile

Description

Active – The project has reached a stable, usable state and is being actively developed.

More information

https://www.repostatus.org/#active

We provide a Docker image with SOMEF already installed. To run through Docker, you may build the Dockerfile provided in the repository by running:

docker build -t somef .

Or just use the Docker image already built in DockerHub:

docker pull kcapd/somef

Then, to run your image just type:

docker run -it kcapd/somef /bin/bash

And you will be ready to use SOMEF (see section below). If you want to have access to the results we recommend mounting a volume. For example, the following command will mount the current directory as the out folder in the Docker image:

docker run -it --rm -v $PWD/:/out kcapd/somef /bin/bash

If you move any files produced by somef into /out, then you will be able to see them in your current directory.

To run SOMEF, please follow the next steps:

Clone this GitHub repository

git clone https://github.com/KnowledgeCaptureAndDiscovery/somef.git

Install somef (you should be in the folder that you just cloned). Note that for Python 3.7 and 3.8 the module Cython should be installed in advanced (through the command: pip install Cython).

cd somef
pip install -e .

Test SOMEF installation

somef --help

If everything goes fine, you should see:

Usage: somef [OPTIONS] COMMAND [ARGS]...

Options:
  -h, --help  Show this message and exit.

Commands:
  configure  Configure credentials
  describe   Running the Command Line Interface
  version    Show somef version.

SOMEF is available in Pypi!. To install it just type:

pip install somef

• Python 3.9

SOMEF has been tested on Unix, MacOS and Windows Microsoft operating systems

Before running SOMEF for the first time, you must configure it appropriately (you only need to do this once). Run

somef configure

And you will be asked to provide the following:

• A GitHub authentication token [optional, leave blank if not used], which SOMEF uses to retrieve metadata from GitHub. If you don't include an authentication token, you can still use SOMEF. However, you may be limited to a series of requests per hour. For more information, see https://help.github.com/en/github/authenticating-to-github/creating-a-personal-access-token-for-the-command-line
• The path to the trained classifiers (pickle files). If you have your own classifiers, you can provide them here. Otherwise, you can leave it blank

If you want somef to be automatically configured (without GitHUb authentication key and using the default classifiers) just type:

somef configure -a

For showing help about the available options, run:

somef configure --help

Which displays:

Usage: somef configure [OPTIONS]

  Configure GitHub credentials and classifiers file path

Options:
  -a, --auto  Automatically configure SOMEF
  -h, --help  Show this message and exit.

If you update SOMEF to a newer version, we recommend you configure again the library (by running somef configure). The rationale is that different versions may rely on classifiers which may be stored in a different path.

The following command extracts all metadata available from https://github.com/dgarijo/Widoco/.

somef describe -r https://github.com/dgarijo/Widoco/ -o test.json -t 0.8

Try SOMEF in Binder with our sample notebook:

• <See full documentation at https://somef.readthedocs.io/en/latest/

• https://somef.readthedocs.io/