curation workflow automation and coordination
Visit https://HOST:PORT/bookmarklet and follow the instructions.
Visit an article that contains RRIDs, click the bookmarklet
The found RRIDs are logged to the JavaScript console
The found RRIDs are logged to timestamped files, along with the text and html of the article that was scanned for RRIDs
As root.
layman -a tgbugs-overlay
emerge scibot
rc-config add scibot-bookmarklet default
vim /etc/conf.d/scibot-bookmarklet # set username, group, api key, etc.
/etc/init.d/scibot-bookmarklet start
Set export PATH=~/.local/bin:${PATH}
in ~/.bashrc
sudo apt-get install build-essential python3-dev libxml2-dev libxslt1-dev
pip3 install --user pip pipenv
git clone https://github.com/SciCrunch/scibot.git
cd scibot && pipenv install --skip-lock
pipenv shell
to get an environment with acess to all the required libraries.python scibot/export.py
.Building the rpm
pushd resources/rpmbuild
rpmbuild --nodeps --define "_topdir `pwd`" -ba SPECS/scibot.spec
popd
Once this is done scp the rpm to the host.
Also scp the ssl certs over, or use letsencrypt to obtain a cert.
If you are using using a cert from another registrar you may need to
bundle your certs cat my-cert.crt existing-bundle.crt > scicrunch.io.crt
(see https://gist.github.com/bradmontgomery/6487319 for details)
See nginx.conf
for details on where to put the certs after scping them over.
Install steps run as root or via sudo.
amazon-linux-extras install nginx1.12
yum install scibot-9999-0.noarch.rpm # update with yum reinstall
pip3 install pipenv wheel
vim /etc/systemd/system/scibot-bookmarklet.service.d/env.conf # set api keys etc
Install scibot codebase as the scibot user
git clone https://github.com/SciCrunch/scibot.git
pushd scibot
pipenv install --skip-lock
Hopefully this step will become simpler once we start pushing releases.
pipenv install scibot
or alternately it may also be possible to package
everything we need in the rpm and only install that. With none of the other
steps needed at all.
Start services as root
systemctl start nginx scibot-bookmarklet-sync scibot-bookmarklet
On the scibot host
sudo su scibot -
pushd scibot
echo "$(date -Is) $(git rev-parse HEAD)" >> ~/previous-scibot-hashes
git pull
mv Pipfile.lock "Pipefile.lock.$(date -Is)"
~/.local/bin/pipenv install --skip-lock
Restart as root
systemctl restart scibot-bookmarklet-sync scibot-bookmarklet
Install steps
sudo yum install gcc libxml2 libxml2-devel libxslt libxslt-devel python36 python36-devel python36-pip
sudo alternatives --set python /usr/bin/python3.6
sudo pip install pipenv
git clone https://github.com/SciCrunch/scibot.git
cd scibot && python3.6 setup.py wheel && pipenv install dist/*.whl
export SCIBOT_USERNAME=someusername
export SCIBOT_GROUP=somegroupname
unset HISTFILE
export SCIBOT_API_TOKEN=sometoken
export SCIBOT_SYNC=somerandomnumber
(e.g. run head -c 100 /dev/urandom | tr -dc 'a-zA-Z0-9'
every time)pipenv run scibot-server
you should create a link to the log files folder in ~/scibot/To set up scibot for development (for example if you want to run manual releases)
brew
)git clone https://github.com/tgbugs/scibot.git
pushd scibot
pip3 install --user -e .
will install requirements and register the
scibot folder that is under version control with python as the scibot module.popd
You should change lol
to something less guessable even if it is only
running on localhost.
Run the following blocks in two separate terminals and connect to
https://localhost:4443/bookmarklet
. If you try http
you will get
a connection error.
You will need to generate the self signed certs using openssl as
described in the comments in bookmarklet.py::main().
Alternately comment out the ssl wrapping of the socket and use http
.
SCIBOT_SYNC=lol python -m scibot.sync
SCIBOT_USERNAME=scibot \
SCIBOT_GROUP=dev-group \
SCIBOT_GROUP2=dev-group \
SCIBOT_GROUP_STAGING=__world__ \
SCIBOT_API_TOKEN=hypothesis-api-key \
SCIBOT_SYNC=lol \
python -m scibot.bookmarklet
Make sure you have >=python3.6 and pip installed. Clone the repo and
run python setup.py develop --user
.
SciBot adheres to the Contributor Covenant: https://www.contributor-covenant.org/