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@judell judell/mmr.py
Last active Sep 27, 2018

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monthly morphometry report
import requests, re, json, types, traceback
class HypothesisAnnotation:
def __init__(self, row):
"""Encapsulate relevant parts of one row of a Hypothesis API search."""
self.tags = []
if row.has_key('tags') and row['tags'] is not None:
self.tags = row['tags']
if isinstance(self.tags, types.ListType):
self.tags = [t.strip() for t in self.tags]
self.text = ''
if row.has_key('text'):
self.text = row['text']
self.target = []
if row.has_key('target'):
self.target = row['target']
self.start = self.end = self.prefix = self.exact = self.suffix = None
try:
if isinstance(self.target,list) and len(self.target) and self.target[0].has_key('selector'):
selectors = self.target[0]['selector']
for selector in selectors:
if selector.has_key('type') and selector['type'] == 'TextQuoteSelector':
try:
self.prefix = selector['prefix']
self.exact = selector['exact']
self.suffix = selector['suffix']
except:
traceback.print_exc()
if selector.has_key('type') and selector['type'] == 'TextPositionSelector' and selector.has_key('start'):
self.start = selector['start']
self.end = selector['end']
if selector.has_key('type') and selector['type'] == 'FragmentSelector' and selector.has_key('value'):
self.fragment_selector = selector['value']
except:
print traceback.format_exc()
canonical_url = 'http://www.ncbi.nlm.nih.gov/pubmed/26142024' # original annotated version
alternate_url = 'http://jonudell.net/h/david_kennedy_example.html' # annotated with suggested tags and conventions
query_url = 'https://hypothes.is/api/search?uri=%s' % alternate_url
text = requests.get(query_url).text.decode('utf-8')
rows = json.loads(text)['rows']
h_annotations = [HypothesisAnnotation(row) for row in rows]
def filter_tags_by_prefix(tags, tag_prefix):
return [tag for tag in tags if tag.lower().startswith(tag_prefix.lower())]
def has_tag_starting_with(h_annotation, tag_prefix):
filtered = filter_tags_by_prefix(h_annotation.tags, tag_prefix)
return len(filtered) > 0
def get_tag_starting_with(h_annotation, tag_prefix):
filtered = filter_tags_by_prefix(h_annotation.tags, tag_prefix)
if len(filtered) > 0:
return filtered[0]
else:
return None
def select_annotations_with_tag_prefix(rows, tag_prefix):
return [h_annotation for h_annotation in h_annotations if has_tag_starting_with(h_annotation, tag_prefix)]
def make_interpretation_element(h_annotations, tag_prefix):
list = []
h_annotations = select_annotations_with_tag_prefix(rows, tag_prefix)
for h_annotation in h_annotations:
tag = get_tag_starting_with(h_annotation, tag_prefix)
subtag = tag.split(':')[1]
list.append(subtag + ': ' + h_annotation.exact)
return list
def make_abstract(h_annotations):
html = """
<p><b>Subject Groups:</b> %s</p>
<p><b>Acquisition Methods:</b> %s</p>
<p><b>Analysis Methods:</b> %s</p>
<p><b>Findings:</b> %s</p>""" % (
select_annotations_with_tag_prefix(h_annotations, 'Subject')[0].exact,
', '.join(make_interpretation_element(h_annotations, 'AcquisitionMethod')),
', '.join(make_interpretation_element(h_annotations, 'AnalysisMethod')),
'<ul><li>' + '</li><li>'.join(make_interpretation_element(h_annotations, 'Finding')) + '</li></ul>' )
return html
def subfindings_from_h_annotation(h_annotation):
body = re.sub('\n*<.+>\n*', '', h_annotation.text)
rows = []
chunks = body.split('\n\n')
for chunk in chunks:
fields = chunk.split('\n')
fields = [re.sub('\w+:\s+','',field) for field in fields]
rows.append('<tr><td>' + '</td><td>'.join(fields) + '</td></tr>')
return rows
def make_table(h_annotations):
rows = []
raw_findings = select_annotations_with_tag_prefix(h_annotations, 'Finding')
for raw_finding in raw_findings:
rows += subfindings_from_h_annotation(raw_finding)
html = '<table>'
headers = ['Observation','AnalysisMethod','Location','SubjectGroups']
html += '<tr><th>' + '</th><th>'.join(headers) + '</th></tr>'
html += '\n'.join(rows)
html += '</table>'
return html
html = """<html>
<head>
<title>Monthly Morphology Report for %s</title>
<meta charset="utf-8" />
<style>
body { font-family: verdana; margin: .5in; }
table, td, th { border-collapse: collapse; border: 1px solid black }
td { padding: 6px }
th { padding: 6px; background-color: lightgrey}
</style>
</head>
<body>
<h1>Monthly Morphology Report for %s</h1>
<h2>Abstract Interpretation</h2>
%s
<h2>Tabular Representation</h2>
%s
</body>
</html> """ % ( canonical_url, canonical_url, make_abstract(h_annotations), make_table(h_annotations) )
f = open('mmr.html','w')
f.write(html.encode('utf-8'))
f.close()
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