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Oban #78

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Oban #78

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3f27309
Fixing paths
dosumis Mar 29, 2018
66fa815
Merge branch 'master' of github.com:VirtualFlyBrain/VFB_neo4j
dosumis May 8, 2018
a45e7dc
Added OBAN method to pattern writer.
dosumis May 8, 2018
ccd2bac
Minor indent error
dosumis May 8, 2018
1a90146
Added function to fill in labels where not present. Runs after load f…
dosumis May 14, 2018
8b5771f
Fixed & tested OBAN pattern addition. Unit test still needed.
dosumis May 23, 2018
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97 changes: 90 additions & 7 deletions src/uk/ac/ebi/vfb/neo4j/KB_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

@author: davidos
'''
import uuid
import warnings
import re
import json
Expand Down Expand Up @@ -408,7 +409,7 @@ class node_importer(kb_writer):
e.g. from ontologies, FlyBase, CATMAID.
Constructor: owl_import_updater(endpoint, usr, pwd)
"""

def add_constraints(self, uniqs=None, indexes=None):
"""Specify addition uniqs and indexes via dicts.
{ label : [attributes] } """
Expand Down Expand Up @@ -491,6 +492,7 @@ def update_from_obograph(self, file_path = '', url = ''):
## Update nodes.
self.add_node(labels, IRI, attribute_dict)
self.check_for_obsolete_nodes_in_use()
self.add_missing_labels()
return True

def check_for_obsolete_nodes_in_use(self):
Expand Down Expand Up @@ -554,7 +556,17 @@ def update_current_features_from_FlyBase(self):
def migrate_features_to_new_ids(self, d):
"""STUB"""
return


def add_missing_labels(self):
self.nc.commit_list(["MATCH (n:Property) WHERE (not exists(n.label)) "
"AND (n.is_obsolete = false) AND "
"(exists(n.short_form)) SET n.label = n.short_form",
"MATCH (n:Class) WHERE (not exists(n.label)) "
"AND (n.is_obsolete = false) AND "
"(exists(n.short_form)) SET n.label = n.short_form"
])


class KB_pattern_writer(object):
"""A wrapper class for adding subgraphs following some pre-specified
schema pattern.
Expand Down Expand Up @@ -717,7 +729,6 @@ def add_dataSet(self, name, license, short_form, pub='',
'short_form': short_form,
'description': description,
'dataset_spec_text': dataset_spec_text})
self.ni.commit()
self.ew.add_annotation_axiom(s=name,
r='license',
o=license,
Expand All @@ -736,9 +747,81 @@ def add_dataSet(self, name, license, short_form, pub='',
match_on='short_form',
safe_label_edge=True)




def add_OBAN_assoc(self, s, r, o, source=None, pubs=None, evidence=None, match_on='short_form'):

"""s = subject short_form
r = relation short_form
o = object short_form
source = DB source. e.g. FlyBase
pubs = list of pubs (FBrf or DOI) as strings
evidence = list of evidence types (short_form strings)"""

# requires
# - OBAN to be loaded. - Done.
# - FlyBase evidence to be loaded - we can gradually map this over to something more standard/structured.

# Create assoc node with UUID. Not good for re-use, but that seems OK].

self.ew.add_fact(s, r, o, match_on=match_on) # s,r,o triple

assoc_sf = 'VFBinternal_' + str(uuid.uuid4())
assoc_iri = map_iri('vfb') + assoc_sf

self.ni.add_node(labels=["Individual"],
IRI=assoc_iri)

self.ew.add_named_type_ax(s=assoc_sf,
o='association',
match_on='short_form') # assoc to type

self.ew.add_annotation_axiom(s=assoc_sf,
r='association_has_subject',
o=s,
match_on='short_form') # assoc to subject

self.ew.add_annotation_axiom(s=assoc_sf,
r='association_has_predicate',
o=r,
match_on='short_form') # assoc to predicate

self.ew.add_annotation_axiom(s=assoc_sf,
r='association_has_object',
o=o,
match_on='short_form') # assoc to object

prov_sf = 'VFBinternal_' + str(uuid.uuid4())
prov_iri = map_iri('vfb') + prov_sf

self.ni.add_node(labels=["Individual"],
IRI=prov_iri)

self.ew.add_named_type_ax(s=prov_sf,
o='provenance',
match_on='short_form') # prov to type

self.ew.add_fact(s=assoc_sf,
r='has_provenance',
o=prov_sf,
match_on='short_form') # assoc to prov

if source:
self.ew.add_annotation_axiom(s=prov_sf,
r='source',
o=source,
match_on='short_form') # link to pub

if pubs:
for pub in pubs:
self.ew.add_annotation_axiom(s=prov_sf,
r='references',
o=pub,
match_on='short_form') # link to pub
if evidence:
for e in evidence:
self.ew.add_annotation_axiom(s=prov_sf,
r='RO_0002558',
o=e,
match_on='short_form') # link to evidence

# Specs for a fb_feature_update
## Pull current feature nodes from DB
Expand All @@ -759,4 +842,4 @@ def add_dataSet(self, name, license, short_form, pub='',
# def add_relation_node(self, iri, short_form, label):
# return "MERGE (i:Relation { IRI: '%s'} ) " \
# "SET i.short_form = '%s' " \
# "SET i.label = '%s' " % (iri, short_form, label)
# "SET i.label = '%s' " % (iri, short_form, label)
5 changes: 1 addition & 4 deletions src/uk/ac/ebi/vfb/neo4j/schema/schema_check.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,10 @@
'''

import yaml
import sys
import warnings
import json
import flatdict
import os
print(os.getcwd())
from neo4j_tools import neo4j_connect, results_2_dict_list
from ..neo4j_tools import neo4j_connect, results_2_dict_list

def query(query):
q = nc.commit_list([query])
Expand Down