for docname in base_names:
try:
with Annotations(path_join(directory, docname),
read_only=True) as ann_obj:
tb_count = len([a for a in ann_obj.get_entities()])
rel_count = (len([a for a in ann_obj.get_relations()]) +
len([a for a in ann_obj.get_equivs()]))
event_count = len([a for a in ann_obj.get_events()])
if options_get_validation(directory) == 'none':
docstats.append([tb_count, rel_count, event_count])
else:
# verify and include verification issue count
try:
from projectconfig import ProjectConfiguration
projectconf = ProjectConfiguration(directory)
from verify_annotations import verify_annotation
issues = verify_annotation(ann_obj, projectconf)
issue_count = len(issues)
except:
# TODO: error reporting
issue_count = -1
docstats.append(
[tb_count, rel_count, event_count, issue_count])
except Exception, e:
log_info('Received "%s" when trying to generate stats' % e)
# Pass exceptions silently, just marking stats missing
docstats.append([-1] * len(stat_types))
# Cache the statistics
try:
def get_statistics(directory, base_names, use_cache=True):
# Check if we have a cache of the costly satistics generation
# Also, only use it if no file is newer than the cache itself
cache_file_path = get_stat_cache_by_dir(directory)
try:
cache_mtime = getmtime(cache_file_path)
except OSError as e:
if e.errno == 2:
cache_mtime = -1
else:
raise
try:
if (not isfile(cache_file_path)
# Has config.py been changed?
or getmtime(get_config_py_path()) > cache_mtime
# Any file has changed in the dir since the cache was generated
or any(True for f in listdir(directory)
if (getmtime(path_join(directory, f)) > cache_mtime
# Ignore hidden files
and not f.startswith('.')))
# The configuration is newer than the cache
or getmtime(get_config_path(directory)) > cache_mtime):
generate = True
docstats = []
else:
generate = False
try:
with open(cache_file_path, 'rb') as cache_file:
docstats = pickle_load(cache_file)
if len(docstats) != len(base_names):
Messager.warning(
'Stats cache %s was incomplete; regenerating' %
cache_file_path)
generate = True
docstats = []
except UnpicklingError:
# Corrupt data, re-generate
Messager.warning(
'Stats cache %s was corrupted; regenerating' %
cache_file_path, -1)
generate = True
except EOFError:
# Corrupt data, re-generate
generate = True
except OSError as e:
Messager.warning(
'Failed checking file modification times for stats cache check; regenerating'
)
generate = True
if not use_cache:
generate = True
# "header" and types
stat_types = [("Entities", "int"), ("Relations", "int"), ("Events", "int")]
if options_get_validation(directory) != 'none':
stat_types.append(("Issues", "int"))
if generate:
# Generate the document statistics from scratch
from annotation import JOINED_ANN_FILE_SUFF
log_info('generating statistics for "%s"' % directory)
docstats = []
for docname in base_names:
try:
with Annotations(path_join(directory, docname),
read_only=True) as ann_obj:
tb_count = len([a for a in ann_obj.get_entities()])
rel_count = (len([a for a in ann_obj.get_relations()]) +
len([a for a in ann_obj.get_equivs()]))
event_count = len([a for a in ann_obj.get_events()])
if options_get_validation(directory) == 'none':
docstats.append([tb_count, rel_count, event_count])
else:
# verify and include verification issue count
try:
from projectconfig import ProjectConfiguration
projectconf = ProjectConfiguration(directory)
from verify_annotations import verify_annotation
issues = verify_annotation(ann_obj, projectconf)
issue_count = len(issues)
except BaseException:
# TODO: error reporting
issue_count = -1
docstats.append(
[tb_count, rel_count, event_count, issue_count])
except Exception as e:
log_info('Received "%s" when trying to generate stats' % e)
# Pass exceptions silently, just marking stats missing
docstats.append([-1] * len(stat_types))
# Cache the statistics
try:
with open(cache_file_path, 'wb') as cache_file:
pickle_dump(docstats, cache_file)
except IOError as e:
Messager.warning(
"Could not write statistics cache file to directory %s: %s" %
(directory, e))
return stat_types, docstats
def _enrich_json_with_data(j_dic, ann_obj):
# TODO: figure out if there's a reason for all the str()
# invocations here; remove if not.
# We collect trigger ids to be able to link the textbound later on
trigger_ids = set()
for event_ann in ann_obj.get_events():
trigger_ids.add(event_ann.trigger)
j_dic['events'].append(
[str(event_ann.id),
str(event_ann.trigger), event_ann.args])
for rel_ann in ann_obj.get_relations():
j_dic['relations'].append([
str(rel_ann.id),
str(rel_ann.type),
[(rel_ann.arg1l, rel_ann.arg1), (rel_ann.arg2l, rel_ann.arg2)]
])
for tb_ann in ann_obj.get_textbounds():
#j_tb = [str(tb_ann.id), tb_ann.type, tb_ann.start, tb_ann.end]
j_tb = [str(tb_ann.id), tb_ann.type, tb_ann.spans]
# If we spotted it in the previous pass as a trigger for an
# event or if the type is known to be an event type, we add it
# as a json trigger.
# TODO: proper handling of disconnected triggers. Currently
# these will be erroneously passed as 'entities'
if str(tb_ann.id) in trigger_ids:
j_dic['triggers'].append(j_tb)
# special case for BioNLP ST 2013 format: send triggers
# also as entities for those triggers that are referenced
# from annotations other than events (#926).
if BIONLP_ST_2013_COMPATIBILITY:
if tb_ann.id in ann_obj.externally_referenced_triggers:
try:
j_dic['entities'].append(j_tb)
except KeyError:
j_dic['entities'] = [
j_tb,
]
else:
try:
j_dic['entities'].append(j_tb)
except KeyError:
j_dic['entities'] = [
j_tb,
]
for eq_ann in ann_obj.get_equivs():
j_dic['equivs'].append(
(['*', eq_ann.type] + [e for e in eq_ann.entities]))
for att_ann in ann_obj.get_attributes():
j_dic['attributes'].append([
str(att_ann.id),
str(att_ann.type),
str(att_ann.target), att_ann.value
])
for norm_ann in ann_obj.get_normalizations():
j_dic['normalizations'].append([
str(norm_ann.id),
str(norm_ann.type),
str(norm_ann.target),
str(norm_ann.refdb),
str(norm_ann.refid),
str(norm_ann.reftext)
])
for com_ann in ann_obj.get_oneline_comments():
comment = [
str(com_ann.target),
str(com_ann.type),
com_ann.tail.strip()
]
try:
j_dic['comments'].append(comment)
except KeyError:
j_dic['comments'] = [
comment,
]
if ann_obj.failed_lines:
error_msg = 'Unable to parse the following line(s):\n%s' % (
'\n'.join([
(
'%s: %s' % (
# The line number is off by one
str(line_num + 1),
str(ann_obj[line_num]))).strip()
for line_num in ann_obj.failed_lines
]))
Messager.error(error_msg, duration=len(ann_obj.failed_lines) * 3)
j_dic['mtime'] = ann_obj.ann_mtime
j_dic['ctime'] = ann_obj.ann_ctime
try:
# XXX avoid digging the directory from the ann_obj
import os
docdir = os.path.dirname(ann_obj._document)
if options_get_validation(docdir) in (
'all',
'full',
):
from verify_annotations import verify_annotation
projectconf = ProjectConfiguration(docdir)
issues = verify_annotation(ann_obj, projectconf)
else:
issues = []
except Exception as e:
# TODO add an issue about the failure?
issues = []
Messager.error('Error: verify_annotation() failed: %s' % e, -1)
for i in issues:
issue = (str(i.ann_id), i.type, i.description)
try:
j_dic['comments'].append(issue)
except BaseException:
j_dic['comments'] = [
issue,
]
# Attach the source files for the annotations and text
from os.path import splitext
from annotation import TEXT_FILE_SUFFIX
ann_files = [splitext(p)[1][1:] for p in ann_obj._input_files]
ann_files.append(TEXT_FILE_SUFFIX)
ann_files = sorted([p for p in set(ann_files)])
j_dic['source_files'] = ann_files
def get_annotator_config(directory):
# TODO: "annotator" is a very confusing term for a web service
# that does automatic annotation in the context of a tool
# where most annotators are expected to be human. Rethink.
return ProjectConfiguration(directory).get_annotator_config()
def get_normalization_config(directory):
return ProjectConfiguration(directory).get_normalization_config()
def get_disambiguator_config(directory):
return ProjectConfiguration(directory).get_disambiguator_config()
def get_search_config(directory):
return ProjectConfiguration(directory).get_search_config()
