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

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# # Simple OMEX example

# This notebook an example for creating a COMBINE archive. A COMBINE archive is a bundled package containing all the necessary documents and relevant information for a modeling and simulation project, ensuring that all components are conveniently stored together. The archive is encoded using the Open Modeling EXchange format (OMEX).

# ## 1) Including libraries

# Note: Please change the `colab` flag to `True` if you are using Google Colab.

# In[2]:


colab = False
if colab:
  get_ipython().system('pip install git+https://github.com/combine-org/combine-notebooks')
  get_ipython().system('git clone https://github.com/combine-org/combine-notebooks')
  get_ipython().run_line_magic('cd', '/content/combine-notebooks/notebooks')


# In[38]:


from pathlib import Path

from pymetadata.console import console
from pymetadata.omex import EntryFormat, ManifestEntry, Omex

from combine_notebooks import RESULTS_DIR


# ## 2) Creating a COMBINE archieve

# Creating an empty archive and adding entry for SBML.

# In[39]:


# Create OMEX archive of resources.
omex = Omex()


# Get the file location of our results files. These were generated by other notebooks in this repositiory.  The files we will be adding to our OMEX file include:
#  - hello_world_sbml.xml - a simple SBML model
#  - hello_world_cellml.cellml - a simple CellML model
#  - hello_world_sbgn.png - a diagram showing a simple reacton that has been generated using SBGN
#  - hello_world_sbgn.sbgn - correponding SBGN used to generate the .png file
#  - hello_world_sedml.sedml - a simple simulation experiment described using SED-ML

# In[40]:


# Path to our results
results_dir =  Path(RESULTS_DIR.stem)


# First, lets add our simple SBML file into the COMBINE archieve.

# In[41]:


# Add entry for the SBML model
omex.add_entry(
    entry=ManifestEntry(
        location="./sbml/hello_world_sbml.xml",
        format=EntryFormat.SBML_L3V2,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbml.xml",
)


# Now we'll add our simple CellML model.

# In[42]:


# Add entry for the CellML model
omex.add_entry(
    entry=ManifestEntry(
        location="./cellml/hello_world_cellml.cellml",
        format=EntryFormat.CELLML,
        master=False,
    ),
    entry_path=results_dir / "hello_world_cellml.cellml",
)


# Next lets add entries for both our SBGN file and the png that it generated.

# In[43]:


# Add entry for SBGN file
omex.add_entry(
    entry=ManifestEntry(
        location="./sbgn/hello_world_sbgn.sbgn",
        format=EntryFormat.SBGN,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbgn.sbgn",
)

# Add entry for corresponding png file generated from the SBGN
omex.add_entry(
    entry=ManifestEntry(
        location="./sbgn/hello_world_sbgn.png",
        format=EntryFormat.PNG,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sbgn.png",
)


# Finally, we will add a SED-ML file to the COMBINE archieve.

# In[44]:


# Add entry for the SEDML simulation experiment
omex.add_entry(
    entry=ManifestEntry(
        location="./sedml/hello_world_sedml.sedml",
        format=EntryFormat.SEDML,
        master=False,
    ),
    entry_path=results_dir / "hello_world_sedml.sedml"
)


# ## 3) Write and print the COMBINE archieve

# And we're done creating the OMEX file. Now lets save it.

# In[45]:


RESULTS_DIR.mkdir(parents=True, exist_ok=True)
omex_path = RESULTS_DIR / "combine_hello_world.omex"
omex.to_omex(omex_path)


# We can also use the `console.print` function to display the comtent of the OMEX file.

# In[46]:


console.print(omex)