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

# Prepare the environments with some imports

# In[1]:


from qiime.sdk.workflow import WorkflowTemplate
from qiime.sdk.type.primitive import Int
from feature_table import rarefy
from feature_table.artifact_types.feature_table import FeatureTable, Frequency


# Create an artifact to work with.

# In[3]:


import biom
from qiime.sdk.artifact import Artifact
biom_path = "/Users/caporaso/code/q2d2/example-data/keyboard/q191/otu-table.tsv"

table = biom.load_table(biom_path)
Artifact.save(table, FeatureTable[Frequency], "nothing...", "./table.qtf")


# Instantiate the workflow template (note that the output is a concrete type here, so the fact that ``Signature.__call__`` isn't actually solving anything isn't a problem yet). 

# In[2]:


wt = WorkflowTemplate.from_function(function=rarefy, 
                                    inputs={'table': FeatureTable[Frequency], 'depth': Int}, 
                                    outputs={'rarefied_table': FeatureTable[Frequency]}, 
                                    name="Rarefaction",
                                    doc="Let's rarefy!")


# Instantiate the context. Note that it discovers its artifacts.

# In[5]:


from qiime.q2d3.context import Q2D3Context


# In[6]:


q2d3 = Q2D3Context('./')


# In[7]:


q2d3.data


# Call the context to generate the actual job. Here we're doing some ugly stuff to grab the UUID from ``q2d3.data``, since the UUID is different everytime we run this.

# In[8]:


print(q2d3(wt, {'table': list(q2d3.data.keys())[0]}, {'depth': 42}))


# Now, restart the kernel (see that the cell counts start over) and confirm that the job code does actually work. 

# In[1]:


from qiime.sdk.artifact import Artifact
table = Artifact('./table.qtf').data
depth = 42


# In[2]:


from feature_table._normalize import rarefy
rarefied_table = rarefy(table=table, depth=depth)


# In[3]:


from feature_table.artifact_types.feature_table import Frequency
from feature_table.artifact_types.feature_table import FeatureTable
Artifact.save(rarefied_table, FeatureTable[Frequency], None, '/Users/caporaso/temp/q2d3-test/tmpmct3i3e_.qtf')


# In[4]:


get_ipython().system("tar -xvf '/Users/caporaso/temp/q2d3-test/tmpmct3i3e_.qtf'")


# The table is rarefied! 

# In[5]:


get_ipython().system('biom summarize-table -i tmpmct3i3e_/data/feature-table.biom')


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