#!/usr/bin/env python
# coding: utf-8

# # Simple SBGN example

# This notebook creates a simple model in [SBGN](https://sbgn.github.io/specifications). It models an irreversible reacton. The enzyme catalyses an irreversible metabolic process which consumes substrate S1 and produces product P1. The enzyme is a represented as a macromolecule connected to the process glyph by a catalysis arc. The substrate and the product of the biochemical reaction are represented by simple chemical glyphs. Then we renders a graphical representation and print the SBGN xml.

# ## 1) Including libraries

# In[1]:


import libsbgnpy.libsbgn as libsbgn
from IPython.display import Image
from libsbgnpy.libsbgnTypes import ArcClass, GlyphClass, Language
from combine_notebooks import RESULTS_DIR
from libsbgnpy import render
import os


# ## 2) Declaring the SBGN model

# Create empty sbgn.

# In[2]:


sbgn: libsbgn.sbgn = libsbgn.sbgn()


# Create map, set language and set in sbgn.

# In[3]:


map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)


# Create four glyphs.  We label three of the glyphs as S1, P1, and enzyme.

# In[4]:


g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph0")
g.set_label(libsbgn.label(text="S1"))
g.set_bbox(libsbgn.bbox(y="105.0", x="25.0", h="60.0", w="60.0"))
map.add_glyph(g)

g = libsbgn.glyph(class_=GlyphClass.MACROMOLECULE, id="glyph2")
g.set_label(libsbgn.label(text="enzyme"))
g.set_bbox(libsbgn.bbox(y="30.0", x="115.0", h="40.0", w="80.0"))
map.add_glyph(g)

g = libsbgn.glyph(class_=GlyphClass.PROCESS, id="glyph3")
g.set_bbox(libsbgn.bbox(y="123.0", x="143.0", h="24.0", w="24.0"))
g.add_port(libsbgn.port(y="135.0", x="131.0", id="glyph3.1"))
g.add_port(libsbgn.port(y="135.0", x="179.0", id="glyph3.2"))
map.add_glyph(g)

g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph1")
g.set_label(libsbgn.label(text="P1"))
g.set_bbox(libsbgn.bbox(y="105.0", x="225.0", h="60.0", w="60.0"))
map.add_glyph(g)


# Add three arcs linking the glyphs together.

# In[5]:


a = libsbgn.arc(class_=ArcClass.CONSUMPTION, target="glyph3.1", source="glyph0", id="arc0")
a.set_start(libsbgn.startType(y="135.0", x="85.0"))
a.set_end(libsbgn.endType(y="135.0", x="131.0"))
map.add_arc(a)

a = libsbgn.arc(class_=ArcClass.CATALYSIS, target="glyph3", source="glyph2", id="arc1")
a.set_start(libsbgn.startType(y="70.0", x="155.0"))
a.set_end(libsbgn.endType(y="123.0", x="155.0"))
map.add_arc(a)

a = libsbgn.arc(class_=ArcClass.PRODUCTION, target="glyph1", source="glyph3.2", id="arc2")
a.set_start(libsbgn.startType(y="135.0", x="179.0"))
a.set_end(libsbgn.endType(y="135.0", x="225.0"))
map.add_arc(a)


# ## 3) Write, print and render the generated file 

# Save SBGN model as text and then print that model.

# In[6]:


sbgn_path = str(RESULTS_DIR) + "/hello_world_sbgn.sbgn"
os.makedirs(os.path.dirname(sbgn_path), exist_ok=True)
f_out = sbgn_path
sbgn.write_file(f_out)
xml = open(f_out).read()
print(xml)


# Render the SBGN model.

# In[9]:


# render SBGN
f_png: str = str(RESULTS_DIR) + '/hello_world_sbgn.png'
os.makedirs(os.path.dirname(f_png), exist_ok=True)
render.render_sbgn(sbgn, image_file=f_png, file_format="png")
Image(f_png, width=300)