def parseInteractors(dom, network):
ems = dom.getElementsByTagName("interactor")
interactors = []
#print "interactor tags %d " %len(ems)
for em in ems:
interactor = Entity()
tmp = em.getElementsByTagName("shortLabel")
slabel = tmp[0].firstChild.nodeValue.strip()
slabel = slabel.split('_')[0]
interactor.symbol = slabel
interactor.refs = {}
interactor.name = getText(em, 'fullName')
setPrimaryRef(em, interactor)
if 'uniprotkb' in interactor.refs:
interactor._id = "enti_up_%s" %(interactor.refs['uniprotkb'])
else:
interactor._id = idtool.generate("entity")
interactor.refs['intact'] = em.getAttribute('id')
interactor.group = getText( em.getElementsByTagName("interactorType")[0], 'shortLabel')
interactors.append(interactor)
network.entities = interactors
def parseInteractors(dom, network):
ems = dom.getElementsByTagName("interactor")
interactors = []
#print "interactor tags %d " %len(ems)
for em in ems:
interactor = Entity()
tmp = em.getElementsByTagName("shortLabel")
slabel = tmp[0].firstChild.nodeValue.strip()
slabel = slabel.split('_')[0]
interactor.symbol = slabel
interactor.refs = {}
interactor.name = getText(em, 'fullName')
setPrimaryRef(em, interactor)
if 'uniprotkb' in interactor.refs:
interactor._id = "enti_up_%s" % (interactor.refs['uniprotkb'])
else:
interactor._id = idtool.generate("entity")
interactor.refs['intact'] = em.getAttribute('id')
interactor.group = getText(
em.getElementsByTagName("interactorType")[0], 'shortLabel')
interactors.append(interactor)
network.entities = interactors
def __init__(self, data=None):
if(data):
if(isinstance(data, dict)):
for d in data: self.__setattr__(d, data[d])
else:
raise Exception("Invalid initialization data: %s" %data)
#self.update(data)
else:
self.create_tm = getTime()
self.tm = time.time()
#self.id = self._id if self._id else None
if not self._id: self._id= idtool.generate(self._col)
def __init__(self, data=None):
if (data):
if (isinstance(data, dict)):
for d in data:
self.__setattr__(d, data[d])
else:
raise Exception("Invalid initialization data: %s" % data)
#self.update(data)
else:
self.create_tm = getTime()
self.tm = time.time()
#self.id = self._id if self._id else None
if not self._id: self._id = idtool.generate(self._col)
def activate(req, post_id=None):
"""
This handles the case when seller accepts invitation and clicks the link
"""
post_id = post_id or _getPostId(req)
post = _getPost(req, post_id)
item = Item.collection.find_one({'post_id': post._id})
if(not item):
item = Item({'hello':1})
item._id = idtool.generate("item")
item.post_id = post._id
item.save()
#post.sellervisits = post.sellervisits+1 if ('sellervisits' in post) else 1
#post.mongo_update()
item.id = item._id
post.update(item)
_fillContext(post)
ctx = getContext()
ctx.template = 'adedit.html'
ctx.item = item
return renderResponse()
def load_pubmeds(ids=None):
ids = ids.split(",") if ids else demo_pubmeds
url = "http://togows.dbcls.jp/entry/pubmed/$ID?format=xml"
"""
pub={ '_id':'',
'name':'',
'refs':{ 'pubmed': '' },
'abstract':'',
'local': 0,
'url':'',
'published': 1,
'authors':[]
}
"""
pc = mongo.getCollection('people')
try:
pc.create_index([("last", 1), ("middle",1), ("first",1)], unique=True)
except:
pass
pubs = []
peoples = []
for pid in pubmeds:
try:
uri = url.replace('$ID', pid)
print "Loading %s" %uri
doc = XML2Dict().fromurl(uri)
#print doc
article = doc['PubmedArticleSet']['PubmedArticle']['MedlineCitation']['Article']
article = doc.PubmedArticleSet.PubmedArticle.MedlineCitation.Article
pub = Publication()
pub._id = "publ_pubmed%s" % (pid)
pub.refs= {'pubmed': pid}
pub.name= article['ArticleTitle']['value'] if article.ArticleTitle else ''
pub.abstract = ''
if article.Abstract and article.Abstract.AbstractText:
texts = [ article.Abstract.AbstractText ] if not isinstance(article.Abstract.AbstractText, list) else article.Abstract.AbstractText
pub.abstract= "\n\n".join([ text['value'] for text in texts ])
pub.language=article['Language']['value'] if article.Language else ''
pubs.append(pub)
pub.authors=[]
authors = article['AuthorList']['Author']
for author in authors:
people = {'first': author.ForeName.value if author.ForeName and author.ForeName.value else '',
'last': author.LastName.value if author.LastName and author.LastName.value else '',
'middle': author.Initials.value if author.Initials and author.Initials.value else '' }
if not people['last']: continue
people['namekey'] = "%s.%s.%s" %(people['first'].lower(), people['middle'].lower(), people['last'].lower())
people['_id'] = idtool.generate('peop')
try:
pc.insert(people, safe=True)
print "Inserted %s" %people
except:
del people['_id']
people = pc.find_one(people)
if people:
pc.update({'_id':people['_id']}, {'$addToSet': {'publications':pub._id}}, safe=True)
pub.authors.append(people)
#print authors
except:
print "ERROR: %s" %traceback.format_exc()
pubc = mongo.getCollection('publication')
for pub in pubs:
try:
pubc.insert(pub)
print "Inserted pub: %s" %pub
except:
print "ERROR %s" %traceback.format_exc()
log("Done")
return pubs
def load_pubmeds(ids=None):
ids = ids.split(",") if ids else demo_pubmeds
url = "http://togows.dbcls.jp/entry/pubmed/$ID?format=xml"
"""
pub={ '_id':'',
'name':'',
'refs':{ 'pubmed': '' },
'abstract':'',
'local': 0,
'url':'',
'published': 1,
'authors':[]
}
"""
pc = mongo.getCollection('people')
try:
pc.create_index([("last", 1), ("middle", 1), ("first", 1)],
unique=True)
except:
pass
pubs = []
peoples = []
for pid in pubmeds:
try:
uri = url.replace('$ID', pid)
print "Loading %s" % uri
doc = XML2Dict().fromurl(uri)
#print doc
article = doc['PubmedArticleSet']['PubmedArticle'][
'MedlineCitation']['Article']
article = doc.PubmedArticleSet.PubmedArticle.MedlineCitation.Article
pub = Publication()
pub._id = "publ_pubmed%s" % (pid)
pub.refs = {'pubmed': pid}
pub.name = article['ArticleTitle'][
'value'] if article.ArticleTitle else ''
pub.abstract = ''
if article.Abstract and article.Abstract.AbstractText:
texts = [
article.Abstract.AbstractText
] if not isinstance(article.Abstract.AbstractText,
list) else article.Abstract.AbstractText
pub.abstract = "\n\n".join([text['value'] for text in texts])
pub.language = article['Language'][
'value'] if article.Language else ''
pubs.append(pub)
pub.authors = []
authors = article['AuthorList']['Author']
for author in authors:
people = {
'first':
author.ForeName.value
if author.ForeName and author.ForeName.value else '',
'last':
author.LastName.value
if author.LastName and author.LastName.value else '',
'middle':
author.Initials.value
if author.Initials and author.Initials.value else ''
}
if not people['last']: continue
people['namekey'] = "%s.%s.%s" % (people['first'].lower(),
people['middle'].lower(),
people['last'].lower())
people['_id'] = idtool.generate('peop')
try:
pc.insert(people, safe=True)
print "Inserted %s" % people
except:
del people['_id']
people = pc.find_one(people)
if people:
pc.update({'_id': people['_id']},
{'$addToSet': {
'publications': pub._id
}},
safe=True)
pub.authors.append(people)
#print authors
except:
print "ERROR: %s" % traceback.format_exc()
pubc = mongo.getCollection('publication')
for pub in pubs:
try:
pubc.insert(pub)
print "Inserted pub: %s" % pub
except:
print "ERROR %s" % traceback.format_exc()
log("Done")
return pubs