def test_insert_geo(self):
dataset = Dataset('GDS987').populate()
Word2Geo.insert_geo(dataset)
w2gs = list(Word2Geo.mongo().find({'geo_id': dataset.geo_id}))
self.assertEqual(len(w2gs), 249)
def test_insert_geo(self):
dataset=Dataset('GDS987').populate()
Word2Geo.insert_geo(dataset)
w2gs=list(Word2Geo.mongo().find({'geo_id': dataset.geo_id}))
self.assertEqual(len(w2gs), 249)
def test_get_field_words(self):
dataset = Dataset('GDS987').populate()
words = Word2Geo.get_field_words(dataset)
expected = {
"description": [
u'analysis', u'of', u'kidneys', u'from', u'adult', u'renal',
u'transplant', u'recipients', u'subjected', u'to',
u'calcineurin', u'inhibitor-free', u'immunosuppression',
u'using', u'sirolimus', u'patients', u'treated', u'with',
u'sirolimus', u'have', u'a', u'lower', u'prevalence', u'of',
u'chronic', u'allograft', u'nephropathy', u'compared', u'to',
u'those', u'treated', u'with', u'cyclosporine', u'a',
u'calcineurin', u'inhibitor'
],
"title": [
'kidney', u'transplant', u'response', u'to', u'calcineurin',
u'inhibitor-free', u'immunosuppression', u'using', u'sirolimus'
],
"summary": []
}
# warn("words[title](%d)=%s" % (len(words['title']), words['title']))
for tag, n_words in {
"description": 105,
"title": 9 + 8 + 7,
"summary": 0
}.items():
self.assertEqual(len(words[tag]),
n_words,
msg="%s: got: %d, expected: %d" %
(tag, len(words[tag]), n_words))
def insert_words(geo, words):
'''
geo: GEO object
words: dict [k=source (aka 'tag'); v=list of words (maybe with dups)]
Creates records with keys [geo_id, word, source, count], adds to db
'''
mongo=Word2Geo.mongo()
mongo.remove({'geo_id': geo.geo_id}) # remove the record for this geo
totals=dict() # k=source, v=count
for source, words in words.items():
for word in words:
query={'geo_id':geo.geo_id, 'word':word, 'source':source}
record=mongo.find_one(query)
if record:
if 'count' in record: record['count']+=1
else: record['count']=1
else: # record not found, construct it from query:
record=query
record['count']=1
mongo.save(record)
try: totals[source]+=1
except: totals[source]=1
return totals
def test_get_field_words(self):
geo_id='GSE10072'
geo=Factory().newGEO(geo_id)
words=Word2Geo.get_field_words(geo)
self.assertEqual(len(words['title']), 42)
self.assertEqual(len(words['description']), 0)
self.assertEqual(len(words['summary']), 738) # not quite sure why this isn't 741
def test_get_field_words(self):
geo_id = "GSE10072"
geo = Factory().newGEO(geo_id)
words = Word2Geo.get_field_words(geo)
self.assertEqual(len(words["title"]), 42)
self.assertEqual(len(words["description"]), 0)
self.assertEqual(len(words["summary"]), 738) # not quite sure why this isn't 741
def test_get_pubmed_words(self):
dataset=Dataset('GDS987').populate()
self.assertEqual(dataset.pubmed_id, str(15476476))
words=Word2Geo.get_pubmed_words(dataset.pubmed_id)
for tag, n_words in {"MeshHeading":86 , "AbstractText":412, "ArticleTitle":34}.items():
self.assertIn(tag, words)
self.assertIsInstance(words[tag], list)
# warn("words[%s] (%d): %s" % (tag, len(words[tag]), words[tag]))
self.assertEqual(len(words[tag]), n_words)
def test_get_field_words(self):
dataset=Dataset('GDS987').populate()
words=Word2Geo.get_field_words(dataset)
expected={"description" : [u'analysis', u'of', u'kidneys', u'from', u'adult', u'renal', u'transplant', u'recipients', u'subjected', u'to', u'calcineurin', u'inhibitor-free', u'immunosuppression', u'using', u'sirolimus', u'patients', u'treated', u'with', u'sirolimus', u'have', u'a', u'lower', u'prevalence', u'of', u'chronic', u'allograft', u'nephropathy', u'compared', u'to', u'those', u'treated', u'with', u'cyclosporine', u'a', u'calcineurin', u'inhibitor'],
"title" : ['kidney', u'transplant', u'response', u'to', u'calcineurin', u'inhibitor-free', u'immunosuppression', u'using', u'sirolimus'],
"summary" : []}
# warn("words[title](%d)=%s" % (len(words['title']), words['title']))
for tag, n_words in {"description": 105, "title": 9+8+7, "summary": 0}.items():
self.assertEqual(len(words[tag]), n_words, msg="%s: got: %d, expected: %d" % (tag, len(words[tag]), n_words))
def test_get_pubmed_words(self):
dataset = Dataset('GDS987').populate()
self.assertEqual(dataset.pubmed_id, str(15476476))
words = Word2Geo.get_pubmed_words(dataset.pubmed_id)
for tag, n_words in {
"MeshHeading": 86,
"AbstractText": 412,
"ArticleTitle": 34
}.items():
self.assertIn(tag, words)
self.assertIsInstance(words[tag], list)
# warn("words[%s] (%d): %s" % (tag, len(words[tag]), words[tag]))
self.assertEqual(len(words[tag]), n_words)
def test_insert_GSE10072(self):
series=Series('GSE10072').populate()
Word2Geo.insert_geo(series)
import sys, os
sys.path.append(os.path.join(os.environ['AUREA_HOME'], 'src'))
sys.path.append(os.path.join(os.environ['TRENDS_HOME'], 'pylib'))
import GEO
from GEO.word2geo import Word2Geo
from warn import *
for cls in [
GEO.Series.Series, GEO.Dataset.Dataset, GEO.DatasetSubset.DatasetSubset
]:
#for cls in [GEO.Series.Series, GEO.Dataset.Dataset]:
cursor = cls.mongo().find()
for record in cursor:
geo = cls(record)
warn("inserting %s" % (geo.geo_id))
Word2Geo.insert_geo(geo)
break
def test_insert_GSE10072(self):
series = Series('GSE10072').populate()
Word2Geo.insert_geo(series)
import sys, os
sys.path.append(os.path.join(os.environ['AUREA_HOME'], 'src'))
sys.path.append(os.path.join(os.environ['TRENDS_HOME'], 'pylib'))
import GEO
from GEO.word2geo import Word2Geo
from warn import *
for cls in [GEO.Series.Series, GEO.Dataset.Dataset, GEO.DatasetSubset.DatasetSubset]:
#for cls in [GEO.Series.Series, GEO.Dataset.Dataset]:
cursor=cls.mongo().find()
for record in cursor:
geo=cls(record)
warn("inserting %s" % (geo.geo_id))
Word2Geo.insert_geo(geo)
break
