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

# # Tutorial: Describe Neuroscience Dataset using MINDS

# ## Initialize and configure

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get_ipython().system('pip install nexusforge==0.7.0')


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get_ipython().system('pip install allensdk')


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get_ipython().system('pip install neurom[plotly]==3.0.1')


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get_ipython().system('pip install --upgrade nest-asyncio==1.5.4')


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get_ipython().system('pip install --upgrade jinja2')


# ### Get an authentication token

# The [Nexus sandbox application](https://sandbox.bluebrainnexus.io) can be used to get a token:
# 
# - Step 1: From the [web page](https://sandbox.bluebrainnexus.io), click on the login button in the top right corner and follow the instructions on screen.
# 
# - Step 2: Once logged in, click on the button on the top right that displays your GitHub username. From the dropdown select `Copy token` option. This will copy the token to your clipboard.
# 

# Once a token is obtained, proceed to paste it as the value of the `TOKEN` variable below.
# 
# __Important__: A Nexus token is valid for 8 hours, if your working session is open for more than 8 hours, you may need to refresh the value of the token and reintialize the forge client in the _'Configure a forge client to store, manage and access datasets'_ section below. 

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import getpass


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TOKEN = getpass.getpass()


# ### Configure a forge client to store, manage and access datasets

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import uuid
import base64
import requests
import json
from pathlib import Path

from kgforge.core import KnowledgeGraphForge
from kgforge.specializations.mappings import DictionaryMapping

from allensdk.api.queries.cell_types_api import CellTypesApi
from allensdk.core.cell_types_cache import CellTypesCache


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r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')
dirpath = './rdfmodel'
Path(dirpath).mkdir(parents=True, exist_ok=True)
with open(f'{dirpath}/jsonldcontext.json', 'w') as outfile:
    json.dump(r.json(), outfile)


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ORG = "github-users"
PROJECT = ""  # Provide here the automatically created project name created when you logged into the Nexus sandbox instance.


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forge = KnowledgeGraphForge("https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml",
                            bucket=f"{ORG}/{PROJECT}",
                            endpoint="https://sandbox.bluebrainnexus.io/v1",
                            token=TOKEN,
                            file_resource_mapping='https://raw.githubusercontent.com/BlueBrain/nexus-forge/5580e906eb1df9e3b3970a735b82f609207df717/examples/configurations/nexus-store/file-to-resource-mapping.hjson'))


# ## Download datasets from Allen Cell Types Database

# ### Download mouse neuron morphology from the Allen Cell Types Database

# We will be downloading mouse neuron morphology data from the [Allen Cell Types Database](https://celltypes.brain-map.org/). The [AllenSDK](https://allensdk.readthedocs.io/en/latest/) can be used for data download.

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ALLEN_DIR = "allen_cell_types_database"


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ctc = CellTypesCache(manifest_file=f"{ALLEN_DIR}/manifest.json")


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MAX_CELLS = 1
SPECIES = CellTypesApi.MOUSE


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nm_allen_identifiers = [cell["id"] for cell in ctc.get_cells(species=[SPECIES], require_reconstruction = True)][:MAX_CELLS]
print(f"Selected a mouse neuron with identifier: {nm_allen_identifiers}")


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with open(f"{ALLEN_DIR}/cells.json") as f:
    allen_cell_types_metadata = json.load(f)


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nm_allen_metadata = [neuron for neuron in allen_cell_types_metadata if neuron["specimen__id"] in nm_allen_identifiers]


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print(f"Metadata of the neuron {nm_allen_identifiers}:")
nm_allen_metadata


# ### Download one mouse neuron morphology reconstructed from the selected neuron

# We will be downloading one mouse neuron morphology from the [Allen Cell Types Database](https://celltypes.brain-map.org/) using the [AllenSDK](https://allensdk.readthedocs.io/en/latest/).

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for identifier in nm_allen_identifiers:
    ctc.get_reconstruction(identifier)


# ### Download one mouse neuron electrophysiology recording from the selected neuron

# We will be downloading one mouse neuron electrophysiology from the [Allen Cell Types Database](https://celltypes.brain-map.org/) using the [AllenSDK](https://allensdk.readthedocs.io/en/latest/).

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for identifier in nm_allen_identifiers:
    ctc.get_ephys_data(identifier)


# ## Transform Allen Cell Types Database Metadata to [Neuroshapes' MINDS](https://bbp-nexus.epfl.ch/datamodels/class-schemadataset.html) metadata

# ### Map the Allen Cell Types Database neuron morphologies metadata to Neuroshapes

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allen_nm_mapping = DictionaryMapping.load("https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson")
nm_allen_resources = forge.map(nm_allen_metadata, allen_nm_mapping, na='')


# ### Map the Allen Cell Types Database neuron electrophysiology recording to Neuroshapes

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allen_ephys_mapping = DictionaryMapping.load("https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson")
nephys_allen_resources = forge.map(nm_allen_metadata, allen_ephys_mapping, na='')


# ## Register
# 
# If the registration fails, try refreshing the access token and reinitializing the forge client in the _'Configure a forge client to store, manage and access datasets'_ section.

# ### Register the Allen Cell Types Database neuron morphology

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nm_allen_resources.id = forge.format("identifier", "neuronmorphologies", str(uuid.uuid4()))


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forge.register(nm_allen_resources)


# ### Register the Allen Cell Types Database neuron electrophysiology recording

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nephys_allen_resources.id = forge.format("identifier", "traces", str(uuid.uuid4()))


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forge.register(nephys_allen_resources)


# ## Access

# ### Set filters

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_type = "NeuronMorphology"

filters = {"type": _type}


# ### Run Query

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number_of_results = 10  # You can limit the number of results, pass `None` to fetch all the results

data = forge.search(filters, limit=number_of_results)

print(f"{str(len(data))} dataset(s) of type {_type} found")


# ### Display the results as pandas dataframe

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property_to_display = ["id","name","subject","brainLocation.brainRegion.id","brainLocation.brainRegion.label","brainLocation.layer.id","brainLocation.layer.label", "contribution","brainLocation.layer.id","brainLocation.layer.label","distribution.name","distribution.contentUrl","distribution.encodingFormat"]
reshaped_data = forge.reshape(data, keep=property_to_display)

forge.as_dataframe(reshaped_data)


# ### Download

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dirpath = "./downloaded/"
forge.download(data, "distribution.contentUrl", dirpath, overwrite=True)


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ls ./downloaded/


# ### Display a result as 3D Neuron Morphology

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from neurom import load_morphology
from neurom.view.plotly_impl import plot_morph3d
import IPython


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neuron = load_morphology(f"{dirpath}/{data[0].distribution.name}")
plot_morph3d(neuron, inline=False)
IPython.display.HTML(filename='./morphology-3D.html')


# ## Version the dataset
# Tagging a dataset is equivalent to `git tag`. It allows to version a dataset.

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forge.tag(data, value="releaseV112")


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# The version argument can be specified to retrieve the dataset at a given tag.

tagged_data = forge.retrieve(id=data[0].id, version="releaseV112")


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forge.as_dataframe(tagged_data)


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data[0].description="Neuron Morphology from Allen"


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forge.update(data[0])


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non_tagged_data = forge.retrieve(id=data[0].id)


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forge.as_dataframe(non_tagged_data)