Skip to content

Commit

Permalink
Merge pull request #661 from matthiaskoenig/develop
Browse files Browse the repository at this point in the history 
Release pkdb-v0.9.3
  • Loading branch information
@matthiaskoenig
matthiaskoenig authored Sep 30, 2020
2 parents f51604e + 0ce3f95 commit c8f3e0d
Show file tree
Hide file tree
Showing 155 changed files with 5,691 additions and 3,393 deletions.
105 changes: 105 additions & 0 deletions INSTALLATION.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,105 @@

# Installation
PK-DB is deployed via `docker` and `docker-compose`.

## Requirements
To setup the development server
the following minimal requirements must be fulfilled
- `docker`
- `docker-compose`
- `Python3.6`

For elasticsearch the following system settings are required
```
sudo sysctl -w vm.max_map_count=262144
```
To set `vm.max_map_count` persistently change the value in
```
/etc/sysctl.conf
```
## Start development server
To start the local development server
```bash
# clone or pull the latest code
git clone https://github.com/matthiaskoenig/pkdb.git
cd pkdb
git pull

# set environment variables
set -a && source .env.local

# create/rebuild all docker containers
./docker-purge.sh
```
This setups a clean database and clean volumes and starts the containers for `pkdb_backend`, `pkdb_frontend`, `elasticsearch` and `postgres`.
You can check that all the containers are running via
```bash
docker container ls
```
which lists the current containers
```
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
bc7f9204468f pkdb_backend "bash -c '/usr/local…" 27 hours ago Up 18 hours 0.0.0.0:8000->8000/tcp pkdb_backend_1
17b8d243e956 pkdb_frontend "/bin/sh -c 'npm run…" 27 hours ago Up 18 hours 0.0.0.0:8080->8080/tcp pkdb_frontend_1
7730c6fe2210 elasticsearch:6.8.1 "/usr/local/bin/dock…" 27 hours ago Up 18 hours 9300/tcp, 0.0.0.0:9123->9200/tcp pkdb_elasticsearch_1
e880fbb0f349 postgres:11.4 "docker-entrypoint.s…" 27 hours ago Up 18 hours 0.0.0.0:5433->5432/tcp pkdb_postgres_1
```
The locally running develop version of PK-DB can now be accessed via the web browser from
- frontend: http://localhost:8080
- backend: http://localhost:8000

### Fill database
Due to copyright, licensing and privacy issues this repository does not contain any data.
All data is managed via a separate private repository at https://github.com/matthiaskoenig/pkdb_data.
This also includes the curation scripts and curation workflows.

If you are interested in curating data or contributing data please contact us at https://livermetabolism.com.

# Docker
[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database)
In the following typical examples to interact with the PK-DB docker containers are provided.

### Check running containers
To check the running containers use
```bash
watch docker container ls
```

### Interactive container mode
```bash
./docker-interactive.sh
```

### Container logs
To get access to individual container logs use `docker container logs <container>`. For instance to check the
django backend logs use
```bash
docker container logs pkdb_backend_1
```

### Run command in container
To run commands inside the docker container use
```bash
docker-compose run --rm backend [command]
```
or to run migrations
```bash
docker-compose run --rm backend python manage.py makemigrations
```

### Authentication data
The following examples show how to dump and restore the authentication data.

Dump authentication data
```bash
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata auth --indent 2 > ./backend/pkdb_app/fixtures/auth.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata users --indent 2 > ./backend/pkdb_app/fixtures/users.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata rest_email_auth --indent 2 > ./backend/pkdb_app/fixtures/rest_email_auth.json
```

Restore authentication data
```bash
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata auth pkdb_app/fixtures/auth.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata users pkdb_app/fixtures/users.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata rest_email_auth pkdb_app/fixtures/rest_email_auth.json
```
131 changes: 0 additions & 131 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,6 @@ and
* [How to cite](https://github.com/matthiaskoenig/pkdb#how-to-cite)
* [License](https://github.com/matthiaskoenig/pkdb#license)
* [Funding](https://github.com/matthiaskoenig/pkdb#funding)
* [Installation](https://github.com/matthiaskoenig/pkdb#installation)
* [REST API](https://github.com/matthiaskoenig/pkdb#rest-api)
* [Docker interaction](https://github.com/matthiaskoenig/pkdb#docker-interaction)

## Overview
[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database)
Expand Down Expand Up @@ -57,132 +54,4 @@ If you use PK-DB code cite in addition

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1406979.svg)](https://doi.org/10.5281/zenodo.1406979)

## Installation
[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database)
PK-DB is deployed via `docker` and `docker-compose`.

### Requirements
To setup the development server
the following minimal requirements must be fulfilled
- `docker`
- `docker-compose`
- `Python3.6`

For elasticsearch the following system settings are required
```
sudo sysctl -w vm.max_map_count=262144
```
To set `vm.max_map_count` persistently change the value in
```
/etc/sysctl.conf
```
### Start development server
To start the local development server
```bash
# clone or pull the latest code
git clone https://github.com/matthiaskoenig/pkdb.git
cd pkdb
git pull

# set environment variables
set -a && source .env.local

# create/rebuild all docker containers
./docker-purge.sh
```
This setups a clean database and clean volumes and starts the containers for `pkdb_backend`, `pkdb_frontend`, `elasticsearch` and `postgres`.
You can check that all the containers are running via
```bash
docker container ls
```
which lists the current containers
```
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
bc7f9204468f pkdb_backend "bash -c '/usr/local…" 27 hours ago Up 18 hours 0.0.0.0:8000->8000/tcp pkdb_backend_1
17b8d243e956 pkdb_frontend "/bin/sh -c 'npm run…" 27 hours ago Up 18 hours 0.0.0.0:8080->8080/tcp pkdb_frontend_1
7730c6fe2210 elasticsearch:6.8.1 "/usr/local/bin/dock…" 27 hours ago Up 18 hours 9300/tcp, 0.0.0.0:9123->9200/tcp pkdb_elasticsearch_1
e880fbb0f349 postgres:11.4 "docker-entrypoint.s…" 27 hours ago Up 18 hours 0.0.0.0:5433->5432/tcp pkdb_postgres_1
```
The locally running develop version of PK-DB can now be accessed via the web browser from
- frontend: http://localhost:8080
- backend: http://localhost:8000

### Fill database
Due to copyright, licensing and privacy issues this repository does not contain any data.
All data is managed via a separate private repository at https://github.com/matthiaskoenig/pkdb_data.
This also includes the curation scripts and curation workflows.

If you are interested in curating data or contributing data please contact us at https://livermetabolism.com.


## REST API
[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database)
PKDB provides a REST API which allows simple interaction with the database and easy access of data.
An overview over the REST endpoints is provided at [`http://localhost:8000/api/v1/`](http://localhost:8000/api/v1/).

### Query examples
The REST API supports elastisearch queries, with syntax examples
available [here](https://django-elasticsearch-dsl-drf.readthedocs.io/en/latest/basic_usage_examples.html)
* http://localhost:8000/api/v1/comments_elastic/?user_lastname=K%C3%B6nig
* http://localhost:8000/api/v1/characteristica_elastic/?group_pk=5&final=true
* http://localhost:8000/api/v1/characteristica_elastic/?search=group_name:female&final=true
* http://localhost:8000/api/v1/substances_elastic/?search:name=cod
* http://localhost:8000/api/v1/substances_elastic/?search=cod
* http://localhost:8000/api/v1/substances_elastic/?ids=1__2__3
* http://localhost:8000/api/v1/substances_elastic/?ids=1__2__3&ordering=-name
* http://localhost:8000/api/v1/substances_elastic/?name=caffeine&name=acetaminophen

### Suggestion example
In addition suggestion queries are possible
* http://localhost:8000/api/v1/substances_elastic/suggest/?search:name=cod

## Docker interaction
[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database)
In the following typical examples to interact with the PK-DB docker containers are provided.

### Check running containers
To check the running containers use
```bash
watch docker container ls
```

### Interactive container mode
```bash
./docker-interactive.sh
```

### Container logs
To get access to individual container logs use `docker container logs <container>`. For instance to check the
django backend logs use
```bash
docker container logs pkdb_backend_1
```

### Run command in container
To run commands inside the docker container use
```bash
docker-compose run --rm backend [command]
```
or to run migrations
```bash
docker-compose run --rm backend python manage.py makemigrations
```

### Authentication data
The following examples show how to dump and restore the authentication data.

Dump authentication data
```bash
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata auth --indent 2 > ./backend/pkdb_app/fixtures/auth.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata users --indent 2 > ./backend/pkdb_app/fixtures/users.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py dumpdata rest_email_auth --indent 2 > ./backend/pkdb_app/fixtures/rest_email_auth.json
```

Restore authentication data
```bash
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata auth pkdb_app/fixtures/auth.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata users pkdb_app/fixtures/users.json
docker-compose -f $PKDB_DOCKER_COMPOSE_YAML run --rm backend ./manage.py loaddata rest_email_auth pkdb_app/fixtures/rest_email_auth.json
```

&copy; 2017-2020 Jan Grzegorzewski & Matthias König; https://livermetabolism.com.
14 changes: 0 additions & 14 deletions TODO.md
View file

This file was deleted.

Loading

0 comments on commit c8f3e0d

Please sign in to comment.