amiko-web

AmiKo Web — Swiss Drug Compendium with Play Framework 2.9.2

Drug Interaction Check (SDIF)

Drug interactions are powered by SDIF (Swiss Drug Interaction Finder) using a pre-built interactions.db in the sqlite/ directory. Three detection strategies:

1. Substance-level — direct lookup of substance mentions in Fachinformation
2. ATC class-level — 42 pharmacological classes with German keyword matching
3. CYP enzyme — CYP450-mediated interactions (CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP1A2, CYP2C8, CYP2B6)

Route indicators (topisch, i.v., s.c., etc.) and approved combination therapy hints are displayed next to drug names. Severity levels: Kontraindiziert (###), Schwerwiegend (##), Vorsicht (#), Keine Einstufung (-). Severity keywords are synced with SDIF; animal model references (Tiermodell) are deprioritized in context extraction. EPha API provides supplementary risk scoring.

Install Activator

https://www.lightbend.com/activator/download
wget downloads.typesafe.com/typesafe-activator/1.3.10/typesafe-activator-1.3.10.zip
Add it to your Path in .bashrc
export PATH=/usr/local/src/activator-dist-1.3.10/bin:$PATH

Clone the Software

git clone https://github.com/zdavatz/amiko-web.git

Update the Software

cd /usr/local/src/amiko-web
git pull
activator -java-home /usr/local/src/jdk1.8.0_92/
cd /var/www/amiko.oddb.org/
rm amikoweb-1.0-SNAPSHOT.zip
mv /usr/local/src/amiko-web/target/universal/amikoweb-1.0-SNAPSHOT.zip /var/www/amiko.oddb.org/
rm -r /var/www/amiko.oddb.org/amikoweb-1.0-SNAPSHOT
unzip amikoweb-1.0-SNAPSHOT.zip
cp -r /var/www/amiko.oddb.org/amikoweb-1.0-SNAPSHOT/* /var/www/amiko.oddb.org/
vim conf/application.conf
svc -h /service/amiko.oddb.org

Update the database

cd /var/www/amiko.oddb.org/sqlite
rm amiko_db_full_idx_de.db
wget http://pillbox.oddb.org/amiko_db_full_idx_de.zip
unzip amiko_db_full_idx_de.zip
rm amiko_db_full_idx_de.zip
svc -h /service/amiko.oddb.org

Update the interactions database

Rebuild interactions.db using SDIF:

cd /usr/local/src/sdif
cargo run -- build
cp db/interactions.db /var/www/amiko.oddb.org/sqlite/
svc -h /service/amiko.oddb.org

Update Full-Text-Search

wget http://pillbox.oddb.org/amiko_frequency_de.db.zip
unzip amiko_frequency_de.db.zip
mv amiko_frequency_de.db /var/www/amiko.oddb.org/sqlite

Setup Daemontools in /service/amiko.oddb.org

mkdir /var/www/amiko.oddb.org/svc/run
-> #!/bin/sh
-> exec /var/www/amiko.oddb.org/bin/amikoweb -java-home /usr/local/src/jdk1.8.0_92/
ln -s /var/www/amiko.oddb.org/svc/ /service/amiko.oddb.org

Do not show Interactions Tab

edit the file /var/www/amiko.oddb.org/svc/run

#!/bin/sh
cd /var/www/amiko.zurrose.ch
export JAVA_OPTS="-Dfeature.interactions=false"
exec /var/www/amiko.zurrose.ch/bin/amikoweb -java-home /usr/local/src/jdk1.8.0_92/

Setup Daemontools logging

• sudo apt-get install daemontools-run

vim /var/www/amiko.oddb.org/svc/log/run
-> #!/bin/sh
-> exec multilog t ./main

Setup Apache with amiko.oddb.org.conf

<VirtualHost *:80>
  ProxyPreserveHost On
  ServerName amiko.oddb.org
  ProxyPass  /excluded !
  ProxyPass / http://127.0.0.1:9000/
  ProxyPassReverse / http://127.0.0.1:9000/
  Redirect permanent /secure https://amiko.oddb.org
</VirtualHost>

<VirtualHost 62.12.131.45:443>
#<VirtualHost *:80>
  ProxyPreserveHost On
  ServerName amiko.oddb.org
  ProxyPass  /excluded !
  ProxyPass / http://127.0.0.1:9000/
  ProxyPassReverse / http://127.0.0.1:9000/
  SSLEngine on
  SSLCertificateFile /etc/letsencrypt/live/amiko.oddb.org/cert.pem
  SSLCertificateKeyFile /etc/letsencrypt/live/amiko.oddb.org/privkey.pem
  SSLCertificateChainFile /etc/letsencrypt/live/amiko.oddb.org/chain.pem
</VirtualHost>

Setup SSL Encryption with Letsencrypt.org

cd /usr/local/src
https://github.com/certbot/certbot.git
https://github.com/certbot/certbot/blob/master/README.rst

Install Nodejs with nvm

see instructions by creationix

curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash
nvm install 6.9.5

this will install

• node v6.9.5
• npm v3.10.10

Footer Copyright Year

The copyright year in the footer is generated dynamically and always shows the current year.

Generating amikoweb-1.0-SNAPSHOT.zip

In the $SRC Dir type activator. This will build amikoweb-1.0-SNAPSHOT.zip