csachgau/fishBook
1
0
Fork 0
forked from jgrewe/fishbook
Code Issues Pull Requests Releases Wiki Activity

[docs] more more more

Browse Source
This commit is contained in:
Jan Grewe 2020-08-04 14:35:28 +02:00
parent 472f771cb5
commit 32f4f23527
2 changed files with 93 additions and 89 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

99
docs/index.md
View File

@ -1,118 +1,39 @@
# How to use the fishbook # How to use the fishbook
## Requirements ## Requirements & Installation
* Python 3.5+ only, **no** python 2 * Python 3.5+ only, **no** python 2
* [datajoint](https://datajoint.io) to connect to the database and to map python objects to table entries. * [datajoint](https://datajoint.io) to connect to the database and to map python objects to table entries.
* [nixio](https://github.com/g-node/nixpy) to read the relacs-flavored nix files during import or later during data retrieval. * [nixio](https://github.com/g-node/nixpy) to read the relacs-flavored nix files during import or later during data retrieval.
## Installation
### 1) Clone the repository ### Clone the repository
```bash ```shell
>> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git >> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git
``` ```
### 2) Installation ### Install
When installing for development: install for the current user, install as "editable": When installing for development: install for the current user, install as "editable":
```bash ```shell
>> cd fishbook >> cd fishbook
>> pip3 install -e fishbook --user >> pip3 install -e fishbook --user
``` ```
When installing for use: When installing for use:
```bash ```shell
>> pip3 install fishbook --user >> pip3 install fishbook --user
# or, for system-wide installation # or, for system-wide installation
>> sudo pip3 install fishbook >> sudo pip3 install fishbook
``` ```
### Running *fishbook*
### 3) Installing a local database server To run fishbook you need access to a database server. If you have access to one proceed with [configuring](configuration.md) the project. Otherwise, if you want to run it using a local database server see [these instructions](setting_up.md).
When you want to run *fishbook* locally you need to install a local database server (either mariaDB or mysql).
On Ubuntu or Linux mint use *apt* to install the server
```bash ```python
sudo apt update import fishbook as fb
sudo apt install mariadb-server
sudo mysql_secure_installation
``` ```
On Fedora use *dnf*
```bash
sudo dnf update
sudo dnf install mariadb-server
sudo mysql_secure_installation
```
On MacOS the most convenient way is to use [*homebrew*](https://brew.sh) see also [mariadb documentation](https://mariadb.com/kb/en/installing-mariadb-on-macos-using-homebrew/)
```bash
brew install mariadb
mysql.server start
brew services start mariadb # to automatically start the server upon boot
```
On Windows you probably need to download an installer...
Upon installation you should be able to log into the database as root without a password.
```bash
mysql -u root
```
To allow *datajoint* to store stuff on the server you need to:
1. Create a database on the server.
2. Add a user and grant this user read and write access.
### Creating a database
At the moment *fishbook* assumes that your database is called **fish_book**. To create it log into the server
```bash
mysql -u root -p
```
And and execute the following commands
```sql
MariaDB [(none)]> CREATE DATABASE fish_book CHARACTER SET = utf8;
MariaDB [(none)]> GRANT ALL ON fish_book.* TO 'foo'@'localhost' IDENTIFIED BY 'password';
MariaDB [(none)]> FLUSH PRIVILEGES;
```
The first command creates the empty database and sets the Character set to utf8. This is important at least when it comes to *fishbook*. The second row creates a user **foo** and grants that user all rights on all tables of **fish_book**. So far **foo** can only log in from the local machine. In order to grant access also from outsides you need to issue a second command:
```sql
MariaDB [(none)]> GRANT ALL ON fish_book.* TO 'foo'@'%' IDENTIFIED BY 'password';
MariaDB [(none)]> FLUSH PRIVILEGES;
```
From localhost you should now be able to log into the **fish_book** database by
```bash
mysql fish_book -u foo -p
```
From outsides use
```shell
mysql fish_book -h yourhost.yourdomain -u foo -p
```
### Things to remember
* Database engine must be InnoDB, which is default in MariaDB
* **OperationalError: (1071, 'Specified key was too long; max key length is 3072 bytes')**
Caused by a wrong character set check that it is set to utf8:
```sql
ALTER DATABASE `fish_book` CHARACTER SET utf8;
```

83
docs/setting_up.md Normal file
View File

@ -0,0 +1,83 @@
# Installing a local database server
When you want to run *fishbook* locally you need to install a local database server (either mariaDB or mysql).
On Ubuntu or Linux mint use *apt* to install the server
```bash
sudo apt update
sudo apt install mariadb-server
sudo mysql_secure_installation
```
On Fedora use *dnf*
```bash
sudo dnf update
sudo dnf install mariadb-server
sudo mysql_secure_installation
```
On MacOS the most convenient way is to use [*homebrew*](https://brew.sh) see also [mariadb documentation](https://mariadb.com/kb/en/installing-mariadb-on-macos-using-homebrew/)
```bash
brew install mariadb
mysql.server start
brew services start mariadb # to automatically start the server upon boot
```
On Windows you probably need to download an installer...
Upon installation you should be able to log into the database as root without a password.
```bash
mysql -u root
```
To allow *datajoint* to store stuff on the server you need to:
1. Create a database on the server.
2. Add a user and grant this user read and write access.
## Creating a database
At the moment *fishbook* assumes that your database is called **fish_book**. To create it log into the server
```bash
mysql -u root -p
```
And and execute the following commands
```sql
MariaDB [(none)]> CREATE DATABASE fish_book CHARACTER SET = utf8;
MariaDB [(none)]> GRANT ALL ON fish_book.* TO 'foo'@'localhost' IDENTIFIED BY 'password';
MariaDB [(none)]> FLUSH PRIVILEGES;
```
The first command creates the empty database and sets the Character set to utf8. This is important at least when it comes to *fishbook*. The second row creates a user **foo** and grants that user all rights on all tables of **fish_book**. So far **foo** can only log in from the local machine. In order to grant access also from outsides you need to issue a second command:
```sql
MariaDB [(none)]> GRANT ALL ON fish_book.* TO 'foo'@'%' IDENTIFIED BY 'password';
MariaDB [(none)]> FLUSH PRIVILEGES;
```
From localhost you should now be able to log into the **fish_book** database by
```bash
mysql fish_book -u foo -p
```
From outsides use
```shell
mysql fish_book -h yourhost.yourdomain -u foo -p
```
## Things to remember
* Database engine must be InnoDB, which is default in MariaDB
* **OperationalError: (1071, 'Specified key was too long; max key length is 3072 bytes')**
Caused by a wrong character set check that it is set to utf8:
```sql
ALTER DATABASE `fish_book` CHARACTER SET utf8;
```