$ pip install git+https://github.com/ctsit/m3c-tools.git
Obtain a PubMed API token for increased API limits.
To run the tools, you will need a YAML configuration file containing several
properties. See config-example.yaml for an example.
If Postgres is behind a firewall, you can setup an SSH tunnel to connect to it:
$ ssh -L 5432:localhost:5432 stage.vivo.metabolomics.info
Where stage.vivo.metabolomics.info is the host running Postgres and 5432 is
the standard Postgres port.
The prefill command pre-fills the Supplemental tables with necessary
information like people and organizations.
Run it:
$ m3c prefill $CONFIG_PATH
Next, run:
$ m3c generate $CONFIG_PATH
This will produce up to several N-Triples files including: projects.nt, studies.nt, datasets.nt, and people.nt. These files contain the triples for each respective type.
The Publication Fetcher tries to find all authors' publications by using Harvard's Catalyst service or PubMed. Then downloads the XML summaries from PubMed and adds them to the supplemental database. Use the admin page to mark publications for inclusion and exclusion. (At least one PMID and an affiliation is required to use Catalyst).
$ m3c pubfetch $CONFIG_PATH
To start the Admin Froms server, run:
$ m3c serve $CONFIG_PATH
They should be accessible at: http://localhost:5000/
Download the code, setup a virtual environment, and configure it for development.
$ git clone https://github.com/ctsit/m3c-tools.git
$ cd m3c-tools/
$ python3 -m venv venv
$ source venv/bin/activate
$ python setup.py develop
To run all the tests, run:
$ python -m unittest
To run a single test, run:
$ python -m unittest tests/<desired_test>
If you add additional tests, the filename should begin with 'test'.