GPCRdb

https://docs.gpcrdb.org/
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GPCRdb provides data, diagrams and web tools for G protein-coupled receptors (GPCRs), enabling...
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### Start the build process

Source: https://docs.gpcrdb.org/building_a_database.html

Runs the build_all management command with 4 processes and the -t flag for a test build. Remove -t for a full build (not recommended on the development VM).

```bash
/env/bin/python3 manage.py build_all -p 4 -t
```

--------------------------------

### Indentation example: 4 spaces

Source: https://docs.gpcrdb.org/coding_style.html

Shows the required 4-space indentation for loops. The example uses a for loop over proteins and prints each protein.

```python
for protein in proteins:
   print(protein)
```

--------------------------------

### Comment style: # followed by a single space

Source: https://docs.gpcrdb.org/coding_style.html

Demonstrates the correct format for comments: start with a hash and a single space.

```python
# this is a comment
```

--------------------------------

### Python 2 with urllib2 - Fetch protein and alignment

Source: https://docs.gpcrdb.org/web_services.html

Legacy example for Python 2 using urllib2. Fetches a protein and an alignment, parsing JSON and iterating with iteritems().

```python
from urllib2 import urlopen
import json

# fetch a protein
url = 'https://gpcrdb.org/services/protein/adrb2_human/'
response = urlopen(url)
protein_data = json.loads(response.read())
print protein_data
print protein_data['sequence']

# fetch an alignment
url = 'https://gpcrdb.org/services/alignment/protein/adrb1_human,adrb2_human,adrb3_human/TM3,TM5,TM6/'
response = urlopen(url)
alignment_data = json.loads(response.read())
for protein, sequence in alignment_data.iteritems():
    print protein
    print sequence
```

--------------------------------

### Naming conventions: variables, constants, functions, classes

Source: https://docs.gpcrdb.org/coding_style.html

Illustrates naming conventions: lower_case_with_underscores for variables and functions, UPPER_CASE for constants, and InitialCaps for class names. The example also shows a class with an __init__ method.

```python
this_is_a_variable = True

THIS_IS_A_CONSTANT = True

def this_is_a_function():
   pass

class ThisIsAClass:
   __init__(self):
      pass
```

--------------------------------

### Update static file repository

Source: https://docs.gpcrdb.org/reload_database.html

Optional step to collect static files. Not for Vagrant setup.

```bash
<python> manage.py collectstatic
```

--------------------------------

### Import grouping: django, project, other

Source: https://docs.gpcrdb.org/coding_style.html

Demonstrates grouping imports into three categories (django, project, other) separated by one blank line, and followed by 2 blank lines. The example shows imports from django.conf, protein.models, and yaml.

```python
from django.conf import settings

from protein.models import Protein

import yaml


class ...
```

--------------------------------

### Blank lines after class definitions

Source: https://docs.gpcrdb.org/coding_style.html

Shows that class definitions are followed by 2 blank lines. The example includes a class definition and a placeholder for the next class.

```python
class ThisIsAClass:
   __init__(self):
      pass


class ...
```

--------------------------------

### Navigate to project root directory

Source: https://docs.gpcrdb.org/reload_database.html

Change to the project root directory on the virtual machine.

```bash
cd /protwis/sites/protwis
```

--------------------------------

### Run database migrations

Source: https://docs.gpcrdb.org/building_a_database.html

Applies Django migrations to set up the database schema.

```bash
/env/bin/python3 manage.py migrate
```

--------------------------------

### Log into the Vagrant VM and navigate to project directory

Source: https://docs.gpcrdb.org/building_a_database.html

SSH into the Vagrant VM and change to the protwis project directory.

```bash
vagrant ssh
cd /protwis/sites/protwis
```

--------------------------------

### Create and checkout a feature branch

Source: https://docs.gpcrdb.org/git_workflow.html

Creates and switches to a new branch named 'feature/branch-name-describes-ticket'. Use a descriptive branch name.

```bash
git checkout -b feature/branch-name-describes-ticket
```

--------------------------------

### Stage and commit a file

Source: https://docs.gpcrdb.org/git_workflow.html

Adds a specific file to the index and commits it with a message. Always use the -m flag to provide a commit message.

```bash
git add my_file.py
git commit -m "Optimized the performance of my_file"
```

--------------------------------

### Download the newest dump from gpcrdb

Source: https://docs.gpcrdb.org/reload_database.html

Optional step to download the latest database dump from gpcrdb if you don't already have one.

```bash
curl https://files.gpcrdb.org/protwis_sp.sql.gz > ~/protwis.sql.gz
```

--------------------------------

### Stage all modified and new files

Source: https://docs.gpcrdb.org/git_workflow.html

Adds all modified and new files to the index for committing.

```bash
git add --all
```

--------------------------------

### Load the dump into the database

Source: https://docs.gpcrdb.org/reload_database.html

Loads the dump file (either from default location or a chosen one) into the protwis database.

```bash
gunzip -c ~/protwis.sql.gz | psql -U protwis -h localhost -d protwis
```

--------------------------------

### Python 3 with requests - Fetch protein and alignment

Source: https://docs.gpcrdb.org/web_services.html

Recommended approach. Requires the requests library. Fetches a protein by ID and an alignment for multiple proteins and specific transmembrane segments, printing the JSON response and sequence data.

```python
import requests

# fetch a protein
url = 'https://gpcrdb.org/services/protein/adrb2_human/'
response = requests.get(url)
protein_data = response.json()
print(protein_data)
print(protein_data['sequence'])

# fetch an alignment
url = 'https://gpcrdb.org/services/alignment/protein/adrb1_human,adrb2_human,adrb3_human/TM3,TM5,TM6/'
response = requests.get(url)
alignment_data = response.json()
for protein, sequence in alignment_data.items():
    print(protein)
    print(sequence)
```

--------------------------------

### Show current branch

Source: https://docs.gpcrdb.org/git_workflow.html

Displays the current branch name.

```bash
git branch
```

--------------------------------

### Add upstream remote

Source: https://docs.gpcrdb.org/git_workflow.html

Connects the local repository to the main Protwis repository as 'upstream'. Run from the repo root directory.

```bash
git remote add upstream https://github.com/protwis/protwis.git
```

--------------------------------

### Rebuild local BLAST database

Source: https://docs.gpcrdb.org/reload_database.html

Optional step to rebuild the local BLAST database.

```bash
<python> manage.py build_blast_database
```

--------------------------------

### Clone the gpcrdb_data repository

Source: https://docs.gpcrdb.org/building_a_database.html

Clones the gpcrdb_data repository from GitHub into the shared data directory.

```bash
cd ~/protwis_vagrant
git clone https://github.com/protwis/gpcrdb_data.git shared/data/protwis/gpcr
```
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