def show_one_doc_annotations(doc_name, doc_text, annotations, annotator_a,
annotator_b):
from pyConTextNLP.display.html import __insert_color
html = []
color = 'blue'
window_size = 50
html.append("<tr>")
html.append("<td style=\"text-align:left\">{0}</td>".format(doc_name))
html.append(
"<td><a href=\"https://brat.jupyter.med.utah.edu/diff.xhtml?diff=%2Fstudent_folders%2F"
+ annotator_a + "%2F#/student_folders/" + annotator_b + "/" +
doc_name + "\" target=\"_blank\">document view</a></td>")
html.append("</tr>")
for anno in annotations:
# make sure the our snippet will be cut inside the text boundary
begin = anno.start_index - window_size
end = anno.end_index + window_size
begin = begin if begin > 0 else 0
end = end if end < len(doc_text) else len(doc_text)
# render a highlighted snippet
cell = __insert_color(doc_text[begin:end],
[anno.start_index - begin, anno.end_index - end],
color)
# add the snippet into table
html.append("<tr>")
html.append("<td></td>")
html.append("<td style=\"text-align:left\">{0}</td>".format(cell))
html.append("</tr>")
return html
def snippet_markup(doc_name,
anno_doc,
display_types={'SPAN_POSITIVE_PNEUMONIA_EVIDENCE'}):
from pyConTextNLP.display.html import __sort_by_span
from pyConTextNLP.display.html import __insert_color
html = []
color = 'blue'
window_size = 50
html.append("<tr>")
html.append("<td style=\"text-align:left\">{0}</td>".format(doc_name))
html.append("<td></td>")
html.append("</tr>")
for anno in anno_doc.annotations:
if anno.type in display_types:
# make sure the our snippet will be cut inside the text boundary
begin = anno.start_index - window_size
end = anno.end_index + window_size
begin = begin if begin > 0 else 0
end = end if end < len(anno_doc.text) else len(anno_doc.text)
# render a highlighted snippet
cell = __insert_color(
anno_doc.text[begin:end],
[anno.start_index - begin, anno.end_index - end], color)
# add the snippet into table
html.append("<tr>")
html.append("<td></td>")
html.append("<td style=\"text-align:left\">{0}</td>".format(cell))
html.append("</tr>")
return html
def mark_text(txt, nodes, colors={"name": "red", "pet": "blue"}, default_color="black"):
# this function had to be copied and modified from pyConTextNLP.display.html.mark_text
# so that the default_color could be passed through
if not nodes:
return txt
else:
n = nodes.pop(-1)
from pyConTextNLP.display.html import __insert_color
return mark_text(__insert_color(txt,
n.getSpan(),
colors.get(n.getCategory()[0], default_color)),
nodes,
colors=colors,
# this was not being passed through
default_color=default_color)
