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adding debug logging
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@Robbie1977
Robbie1977 authored May 18, 2024
1 parent df66f17 commit 692d2a9
Showing 1 changed file with 45 additions and 44 deletions.
89 changes: 45 additions & 44 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 logging
import warnings
import re
import json
Expand Down Expand Up @@ -990,15 +991,24 @@ def add_anatomy_image_set(self,
anatomy_attributes: Dict of property:value for anatomy node
allow_duplicates: Boolean. If True, allow overwiting of esiting images for flush and replace DataSets
hard_fail: Boolean. If True, throw exception for uknown entitise referenced in args"""


logging.debug("Starting add_anatomy_image_set with parameters:")
logging.debug(f"dataset={dataset}, imaging_type={imaging_type}, label={label}, start={start}, "
f"template={template}, anat_id={anat_id}, anatomical_type={anatomical_type}, "
f"anon_anatomical_types={anon_anatomical_types}, index={index}, center={center}, "
f"anatomy_attributes={anatomy_attributes}, dbxrefs={dbxrefs}, dbxref_strings={dbxref_strings}, "
f"image_filename={image_filename}, force_image_release={force_image_release}, "
f"match_on={match_on}, orcid={orcid}, type_edge_annotations={type_edge_annotations}, "
f"allow_duplicates={allow_duplicates}, hard_fail={hard_fail}")

if anatomy_attributes is None: anatomy_attributes = {}
if not force_image_release: anatomy_attributes['block'] = ["New Images"]
if anon_anatomical_types is None: anon_anatomical_types = []
if dbxrefs is None: dbxrefs = {}
if dbxref_strings is None: dbxref_strings = []

if type_edge_annotations is None: type_edge_annotations = {}

if not template == 'self':
self.ec.roll_entity_check(labels=['Individual'],
match_on=match_on,
Expand All @@ -1012,69 +1022,71 @@ def add_anatomy_image_set(self,
if dbxref_strings:
# Add checking dbxref strings for ':'
dbxrefs.update({x.split(':')[0]:x.split(':')[1] for x in dbxref_strings})

for k in dbxrefs.keys():
self.ec.roll_entity_check(labels=['Individual'],
match_on=match_on,
query=k)

if orcid:
self.ec.roll_entity_check(labels=['Person'],
match_on=match_on,
query=orcid)

for ax in anon_anatomical_types:
self.ec.roll_entity_check(labels=['Property'],
match_on=match_on,
query=ax[0])
self.ec.roll_entity_check(labels=['Class'],
match_on=match_on,
query=ax[1])

if dbxrefs:
for db, acc in dbxrefs.items():
self.ec.roll_dbxref_check(db, acc)
if not self.ec.check(hard_fail=hard_fail):
warnings.warn("Load fail: Cross-referenced enties already exist.")
warnings.warn("Load fail: Cross-referenced entities already exist.")
logging.debug("Cross-referenced entities already exist.")
return False

if not self.ec.check(hard_fail=hard_fail):
warnings.warn("Load fail: Unknown entities referenced.")
logging.debug("Unknown entities referenced.")
return False


if anat_id == None:

if anat_id is None:
anat_id = self.anat_iri_gen.generate(start)
channel_id = self.channel_iri_gen.generate(start)
logging.debug(f"Generated new anat_id: {anat_id}, channel_id: {channel_id}")
else:
anat_id = self.update_anat_id(anat_id)
channel_id = self.update_channel_id(anat_id)
logging.debug(f"Updated anat_id: {anat_id}, channel_id: {channel_id}")
self.ec.roll_new_entity_check(labels=['Individual'],
match_on=match_on,
query=anat_id['short_form'], allow_duplicates=allow_duplicates)
match_on=match_on,
query=anat_id['short_form'], allow_duplicates=allow_duplicates)
if not self.ec.check(hard_fail=hard_fail):
warnings.warn("Load fail: Existing anat_id referenced.")
logging.debug("Existing anat_id referenced.")
return False
anat_id['label'] = label
channel_id['label'] = label + '_c'

anatomy_attributes['label'] = label
self_labels = ["Individual"]
if template == 'self':
self_labels.append("Template")



self.ni.add_node(labels=self_labels,
IRI=anat_id['iri'],
attribute_dict=anatomy_attributes, allow_duplicates=allow_duplicates)
#dataset_short_form = self.ni.nc.commit_list(["MATCH (ds:DataSet) WHERE ds.label = %s RETURN ds.short_form" % dataset])
self.ew.add_annotation_axiom(s=anat_id[match_on],
r='source',
o=dataset,
stype=':Individual',
match_on=match_on,
safe_label_edge=True)

if dbxrefs:
for db, acc in dbxrefs.items():
self.ew.add_annotation_axiom(s=anat_id['short_form'],
Expand All @@ -1084,69 +1096,58 @@ def add_anatomy_image_set(self,
otype=':Individual',
match_on='short_form',
edge_annotations={'accession': [acc]},
safe_label_edge=True
)
safe_label_edge=True)
if orcid:
self.ew.add_annotation_axiom(s=anat_id['short_form'],
r='contributor',
o=orcid,
stype=':Individual',
match_on='short_form') # This assumes matching on short form!

match_on='short_form')
self.ni.add_node(labels=self_labels,
IRI=channel_id['iri'],
attribute_dict={'label': label + '_c'}
)
# Add a query to look up template channel, assuming template anat ind spec
#q = "MATCH (c:Individual)-[:Related { short_form : 'depicts' }]" \
# "->(t:Individual { iri : '%s' }) RETURN c.iri" % template
#x = results_2_dict_list(self.ni.nc.commit_list([q]))
#template = x['c.iri']

# Add typing as channel. This takes no vars so match_on can be fixed.
attribute_dict={'label': label + '_c'})

self.ew.add_named_type_ax(s=channel_id['short_form'],
o='VFBext_0000014',
match_on='short_form')


# Imaging modality - currently works on internal lookup in script. Should probably be dynamic with DB

self.ew.add_anon_type_ax(s=channel_id['iri'],
r=self.relation_lookup['is specified output of'],
o=self.class_lookup[imaging_type])

if anatomical_type:
self.ew.add_named_type_ax(s=anat_id[match_on],
o=anatomical_type,
match_on=match_on,
edge_annotations=type_edge_annotations)
# Add facts

# This takes no vars so match_on can be fixed.

self.ew.add_fact(s=channel_id['iri'],
r=self.relation_lookup['depicts'],
o=anat_id['iri'])

edge_annotations = {}
if index: edge_annotations['index'] = index
if center: edge_annotations['center'] = center
if image_filename: edge_annotations['filename'] = image_filename

if template == 'self':
template = channel_id['short_form']

self.ew.add_fact(s=channel_id['short_form'],
r=get_sf(self.relation_lookup['in register with']),
o=template,
edge_annotations=edge_annotations,
match_on='short_form',
safe_label_edge=True)

for ax in anon_anatomical_types:
self.ew.add_anon_type_ax(s=anat_id[match_on],
r=ax[0],
o=ax[1],
match_on='short_form')


logging.debug("Anatomy image set added successfully.")
return {'channel': channel_id, 'anatomy': anat_id }

def add_dataSet(self, name,
Expand Down

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