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

# # General Information

# This notebook assembles some personal experiences in accessing the [Basic Formal Ontology](https://basic-formal-ontology.org/users.html)(BFO) with [Owlready2](https://owlready2.readthedocs.io/en/latest/index.html).

# In[1]:


import time
print(time.ctime())
get_ipython().run_line_magic('load_ext', 'ipydex.displaytools')


# In[2]:


import owlready2 as owl2


# In[3]:


original_iris = dict(owl2.default_world.graph._abbreviate_d) ##:i


# In[4]:


# bfo = owl2.get_ontology("external_data/bfo.owl").load()

bfo = owl2.get_ontology("http://purl.obolibrary.org/obo/bfo.owl").load()


# In[5]:


all_iris = dict(owl2.default_world.graph._abbreviate_d) ##:i


# In[6]:


new_iris = [key for key in all_iris.keys() if key not in original_iris] ##:i

new_iris[:20]


# In[7]:


classes = list(bfo.classes())

c0 = classes[0]
classes[:10]


# In[8]:


c0.name ##:
c0.label ##:

c0.iri ##:
bfo.base_iri ##:


# ## How to access a class by its `name` (i.e. not by its `label`)?
# 
# ### Manually building the iri
# 
# This requires to know the internal iri-prefix which is not the same as `bfo.base_iri`

# In[9]:


klass = bfo.world["http://purl.obolibrary.org/obo/BFO_0000001"] ##:

klass == c0


# ###  Fixing (hacking) `.base_iri`
# 

# In[10]:


# Inherently, `bfo.BFO_0000001` cannot be resolved due to iri mismatch.
bfo.BFO_0000001 is None


# In[11]:


# changing the base_iri to the string wich is used as prefix in `bfo.world.graph._abbreviate_d`

bfo.base_iri = 'http://purl.obolibrary.org/obo/'


# In[12]:


# now this works as intended
bfo.BFO_0000001 is None ##:

bfo.BFO_0000001


# ### Access via `.search(...)`

# In[13]:


# this does not require to alter the base_iri
bfo.search(iri="*BFO_0000001")


# In[14]:


bfo.search(label="entity")


# In[15]:


bfo.search(label="entity").first().iri


# ## General overview of the entities in BFO

# In[16]:


for e in classes:
    print(e.name, e.label)


# In[17]:


annotation_properties = list(bfo.annotation_properties()) ##:i


# In[18]:


tab = []

for e in annotation_properties:
    try:
        label = e.label
    except TypeError:
        label = "<TypeError>"
    tab.append((e.name, label))


# In[19]:


import tabulate


# In[20]:


print(tabulate.tabulate(tab))


# In[21]:


annotation_properties[2].label


# ---
# 
# isolated problem reproduction (after kernel restart)

# In[1]:


import owlready2 as owl2
bfo = owl2.get_ontology("http://purl.obolibrary.org/obo/bfo.owl").load()

annotation_properties = list(bfo.annotation_properties())

# works -> List[str]
print(annotation_properties[2].label)

# works -> empty list
print(annotation_properties[3].label)

# works not -> TypeError:
print(annotation_properties[0].label)