Workflow for lab management and animal management

This workflow builds a workflow to save the information of lab management and animal management, using the following datajoint elements

This repository provides demonstrations for: Set up a workflow using different elements (see workflow_animal/pipeline.py)

Workflow architecture

The lab and animal management workflow presented here uses components from two DataJoint elements, element-lab, and element-animal assembled together to a functional workflow.

element-lab

element-animal

element-animal contains two modules, subject and genotyping.

subject contains basic information of subjects.

genotyping is designed for labs that handle animal care and genotyping themselves, which is optional.

This workflow serves as an example of the upstream part of a typical data workflow, for examples using these two elements more intact workflows, refer to:

[workflow-array-ephys]https://github.com/datajoint/workflow-array-ephys
[workflow-calcium-imaging]https://github.com/datajoint/workflow-calcium-imaging

Installation instructions

Step 1 - Clone this repository

Launch a new terminal and change directory to where you want to clone the repository
```
cd C:/Projects
```

Clone the repository

git clone https://github.com/datajoint/workflow-animal

Change directory to workflow-animal
```
cd workflow-animal
```

Step 2 - Setup a virtual environment

It is highly recommended (though not strictly required) to create a virtual environment to run the pipeline.

You can install with virtualenv or conda. Below are the commands for virtualenv.
If virtualenv not yet installed, run pip install --user virtualenv
To create a new virtual environment named venv:
```
virtualenv venv
```
To activated the virtual environment:
- On Windows:
```
.\venv\Scripts\activate
```
- On Linux/macOS:
```
source venv/bin/activate
```

Step 3 - Install this repository

From the root of the cloned repository directory: pip install -e .

Note: the -e flag will install this repository in editable mode, in case there's a need to modify the code (e.g. the pipeline.py or paths.py scripts). If no such modification required, using pip install . is sufficient

Step 4 - Jupyter Notebook

ipython kernel install --name=workflow-animal

Step 5 - Configure the `dj_local_conf.json`

At the root of the repository folder, create a new file dj_local_conf.json with the following template:

{
  "database.host": "<hostname>",
  "database.user": "<username>",
  "database.password": "<password>",
  "loglevel": "INFO",
  "safemode": true,
  "display.limit": 7,
  "display.width": 14,
  "display.show_tuple_count": true,
  "custom": {
      "database.prefix": "<neuro_>",
}

Specify database's hostname, username, and password properly.
Specify a database.prefix to create the schemas.

Installation complete

At this point the setup of this workflow is complete.

Interacting with the DataJoint pipeline and exploring data

Connect to database and import tables
```
from workflow_animal.pipeline import *
```
This will create all tables defined in the elements in the database server.
Preview the tables created by calling the classes, for example:
```
lab.Lab()
subject.Subject()
genotyping.GenotypingTest()
```

If required to drop all schemas, the following is the dependency order.

from workflow_animal.pipeline import *

genotyping.schema.drop()
subject.schema.drop()
lab.schema.drop()

For a more in-depth exploration of the tables created, please refer to the example notebook.

Insert into Manual and Lookup tables with Graphical User Interface DataJoint Labbook

DataJoint Neuro also provides a Graphical User Interface DataJoint Labbook to support manual data insertions into DataJoint workflows.

Please refer to the DataJoint Labbook page for instructions to set it up.

Development mode installation

This method allows you to modify the source code for workflow-calcium-imaging, element-calcium-imaging, element-animal, and element-lab.

Launch a new terminal and change directory to where you want to clone the repositories
```
cd C:/Projects
```

Clone the repositories

git clone https://github.com/datajoint/element-lab
git clone https://github.com/datajoint/element-animal
git clone https://github.com/datajoint/workflow-animal

Install each package with the -e option

pip install -e ./workflow-animal
pip install -e ./element-lab
pip install -e ./element-animal

iamamutt/workflow-animal