def map_icd_hierarchy(s, version=9):
s = str(s)
code9 = icd9.search(s)
code10 = icd10.find(s)
if code9 is None and code10 is None:
raise Exception("Invalid ICD code", s)
if version == 9:
if code9 is not None:
return list(reversed([code9.alt_code] + code9.ancestors()))
else:
raise Exception("Invalid ICD version", s)
elif version == 10:
if code10 is not None:
return [code10.chapter, code10.block, code10.code[:3], code10.code]
else:
try:
# Attempt to convert from version 9 to 10
s_ = convert_icd_9_to_10(code9.alt_code)
code = icd10.find(s_)
if code is None:
# Fall back to version 9
return list(reversed([code9.alt_code] + code9.ancestors()))
else:
return [code.chapter, code.block, code.code[:3], code.code]
except:
warnings.warn('Conversion failed: ' + str(s))
return list(reversed([code9.alt_code] + code9.ancestors()))
# raise Exception('Conversion error: ' + str(s))
else:
raise Exception("Invalid ICD version", s)
def test_find_neoplasm():
dx = icd10.find("C10.1")
assert isinstance(dx, icd10.ICD10)
assert dx.code == "C101"
assert dx.billable
assert dx.description == "Malignant neoplasm of anterior surface of epiglottis"
assert not dx.categorical
assert dx.block == "C00-D48"
assert dx.block_description == "Neoplasms"
assert str(dx) == "C10.1"
assert repr(dx) == "<ICD10: C10.1>"
def test_find_salmonella():
dx = icd10.find("A02.1")
assert isinstance(dx, icd10.ICD10)
assert dx.code == "A021"
assert dx.billable
assert dx.description == "Salmonella sepsis"
assert not dx.categorical # Categorical codes are by definition not billable
assert dx.block == "A00-B99"
assert dx.block_description == "Certain infectious and parasitic diseases"
assert str(dx) == "A02.1"
assert repr(dx) == "<ICD10: A02.1>"
def find_ancestor_for_icdcode(icdcode, icdcode2ancestor): if icdcode in icdcode2ancestor: return icdcode2ancestor[icdcode] = [] ancestor = icdcode[:] while len(ancestor) > 2: ancestor = ancestor[:-1] if ancestor[-1]=='.': ancestor = ancestor[:-1] if icd10.find(ancestor) is not None: icdcode2ancestor[icdcode].append(ancestor) return
def annotate(request, from_save=False):
data = request.GET
sid = None
if 'sid' in data:
sid = data['sid']
context = {}
if from_save and sid:
if DocumentSet.objects.get(id=sid).done:
sid = None
# Tasks
context['tasks'] = MetaTask.objects.all().order_by('name')
project = None
document = None
if 'pid' in data:
pid = data['pid']
project = Project.objects.get(id=pid)
document = None
context['document_sets'] = DocumentSet.objects.filter(
project=project).order_by('name')
context['pid'] = pid
else:
# Get first project for this user
pid = Project.objects.filter(members=request.user)[0].id
project = Project.objects.get(id=pid)
document = None
context['document_sets'] = DocumentSet.objects.filter(
project=project).order_by('name')
context['pid'] = pid
if 'did' in data:
did = int(data['did'])
document = Document.objects.get(id=did)
elif project is not None:
if sid is not None:
# Get all ds
document = get_doc(project, sid=sid)
else:
# Get all ds
document = get_doc(project)
if document is not None:
context['documents'] = Document.objects.filter(
document_set=document.document_set).order_by('document_id')
context['active_doc'] = document
else:
if sid is not None:
ds = DocumentSet.objects.get(id=sid)
document = Document.objects.filter(
document_set=ds).order_by('document_id')
context['documents'] = Document.objects.filter(
document_set=document.document_set).order_by('document_id')
context['active_doc'] = document
else:
ds = DocumentSet.objects.filter(
project=project).order_by('name')[0]
document = Document.objects.filter(
document_set=ds).order_by('document_id')[0]
context['documents'] = Document.objects.filter(
document_set=document.document_set).order_by('document_id')
context['active_doc'] = document
text = context['active_doc'].text
_s = context['active_doc'].start_ind
if context['active_doc'].string_orig.lower() in text[_s:].lower():
print("RIGHT VAL")
start = text[_s:].lower().index(
context['active_doc'].string_orig.lower()) + _s
end = start + len(context['active_doc'].string_orig)
elif context['active_doc'].string_orig.lower() in text.lower():
print("SECOND")
start = text.lower().index(context['active_doc'].string_orig.lower())
end = start + len(context['active_doc'].string_orig)
else:
start = 0
end = 0
s_start = max(0, start - 1000)
s_end = min(len(text), end + 1000)
print(s_start)
text = text[s_start:start] + "<span class='ann'>" + text[
start:end] + "</span>" + text[end:s_end]
text = text.replace("\n", "<br />")
context['text'] = text
# Info from MedCAT and some dict
context['pretty_name'] = None
if context['active_doc'].cui.upper() in cdb.cui2pretty_name:
context['pretty_name'] = cdb.cui2pretty_name[
context['active_doc'].cui.upper()]
try:
context['icd'] = icd10.find(
context['active_doc'].document_set.name.upper()).description
context['ch'] = chapter2name[icd10.find(
context['active_doc'].document_set.name.upper()).chapter]
context['ch'] = icd10.find(context['active_doc'].document_set.name.
upper()).chapter + " - " + context['ch']
except:
context['icd'] = "None"
context['ch'] = "None"
doc = context['active_doc']
try:
context['comment'] = Comment.objects.get(document=doc).text
except Exception as e:
print(e)
pass
document = doc
if document.done:
anns = MetaAnnotation.objects.filter(document=document)
context['tasks'][0].real_val = False
for task in context['tasks']:
ann = MetaAnnotation.objects.filter(document=document,
meta_task=task)
if ann:
ann = ann[0]
task.cid = ann.meta_task_value.id
return render(request, 'annotate.html', context)
def download(modeladmin, request, queryset):
if not request.user.is_staff:
raise PermissionDenied
arr = []
tasks = MetaTask.objects.all()
head = [
'doc_id', 'string_orig', 'cui', 'icd10', 'done', 'db_id', 'icd10-ch',
'comment', 'start', 'end', '_start', '_end', 'text'
]
for task in tasks:
head.append(task.name)
arr.append(head)
dss = DocumentSet.objects.filter(project=queryset[0])
for ds in dss:
docs = Document.objects.filter(document_set=ds)
for doc in docs:
try:
comment = Comment.objects.get(document=doc).text
except:
comment = ""
_start = doc.start_ind
_end = doc.end_ind
text = doc.text.lower()
if doc.string_orig.lower() in text[_start:]:
start = text[_start:].index(doc.string_orig.lower()) + _start
end = start + len(doc.string_orig)
elif doc.string_orig.lower() in text:
start = text.index(doc.string_orig.lower())
end = start + len(doc.string_orig)
else:
start = -1
end = -1
if start != -1:
row = [""] * len(head)
row[0] = doc.document_id
row[1] = doc.string_orig
row[2] = doc.cui
row[3] = ds.name
row[4] = doc.done
row[5] = doc.id
row[6] = icd10.find(ds.name.upper()).chapter
row[7] = comment
row[8] = start
row[9] = end
row[10] = _start
row[11] = _end
row[12] = doc.text
anns = MetaAnnotation.objects.filter(document=doc)
for ann in anns:
row[head.index(
ann.meta_task.name)] = ann.meta_task_value.name
arr.append(row)
sio = StringIO()
df = pandas.DataFrame(arr[1:], columns=arr[0])
df.to_csv(sio)
sio.seek(0)
response = HttpResponse(sio, content_type='text/csv')
response['Content-Disposition'] = 'attachment; filename=stat-info.csv'
return response