def assocDataTableEphysVal(dataTableOb):
"""Associates a data table object with ephys concept map objects
"""
dt = dataTableOb
ds = m.DataSource.objects.get(data_table = dt)
robot_user = m.get_robot_user()
if dt.table_text is None:
return
ephysSyns = m.EphysPropSyn.objects.all()
ephysSynList = [e.term.lower() for e in ephysSyns]
tableTag = dt.table_html
soup = BeautifulSoup(''.join(tableTag), 'lxml')
headerTags = soup.findAll('th')
tdTags = soup.findAll('td')
allTags = headerTags + tdTags
for tag in allTags:
origTagText = tag.get_text()
tagText = origTagText.strip()
if 'id' in tag.attrs.keys():
tag_id = str(tag['id'])
else:
tag_id = -1
if len(tagText) == 0:
continue
if has_ascii_letters(tagText) is True:
# SJT Note - Currently doesn't mine terms in synapse stop words list
matched_ephys_ob = match_ephys_header(tagText, ephysSynList)
identified_unit = get_units_from_table_header(tagText)
if matched_ephys_ob:
save_ref_text = origTagText[0:min(len(origTagText),199)]
# create EphysConceptMap object
ephysConceptMapOb = m.EphysConceptMap.objects.get_or_create(ref_text = save_ref_text,
ephys_prop = matched_ephys_ob,
source = ds,
dt_id = tag_id,
#match_quality = matchVal,
changed_by = robot_user,
times_validated = 0,
identified_unit=identified_unit)[0]
def find_ephys_headers_in_table(table_html, early_stopping = False, early_stop_num = 2):
"""Given an html table as input, returns a dict of table cells and their found ephys concept maps
if no ephys concepts found, returns None
"""
if table_html is None:
return
tableTag = table_html
soup = BeautifulSoup(''.join(tableTag), 'lxml')
headerTags = soup.findAll('th')
tdTags = soup.findAll('td')
allTags = headerTags + tdTags
ret_dict = dict()
ephysSyns = m.EphysPropSyn.objects.all()
ephysSynList = [e.term.lower() for e in ephysSyns]
for tag in allTags:
origTagText = tag.get_text()
tagText = origTagText.strip()
if 'id' in tag.attrs.keys():
tag_id = str(tag['id'])
else:
tag_id = -1
if len(tagText) == 0:
continue
if has_ascii_letters(tagText) is True:
# SJT Note - Currently doesn't mine terms in synapse stop words list
matched_ephys_ob = match_ephys_header(tagText, ephysSynList)
# identified_unit = get_units_from_table_header(tagText)
if matched_ephys_ob:
ret_dict[tagText] = matched_ephys_ob
if early_stopping:
if len(ret_dict.keys()) >= early_stop_num:
return ret_dict
if len(ret_dict.keys()) == 0:
return None
return ret_dict
