def main():
start_time = time()
wiki_info_file = 'e:/el/tmpres/demo/wiki-all/wiki-info.pkl'
links_file = 'e:/el/tmpres/demo/wiki-all/links.txt'
description_file = 'e:/el/tmpres/demo/wiki-all/text.txt'
wiki_candidates_file = 'e:/el/tmpres/wiki/dict/name_candidates.pkl'
word_idf_file = 'e:/el/tmpres/demo/word_idf.txt'
tfidf = TfIdf(word_idf_file)
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
wiki_link = WikiLink(wiki_candidates_file, wiki_info, tfidf)
input_file = 'input/00000001.txt'
fin = open(input_file, 'rb')
doc_text = fin.read()
doc_text = doc_text.decode('utf-8')
fin.close()
pos = input_file.rfind('/')
file_name = input_file[pos + 1:]
ner_result_file = os.path.join('output', file_name + '.ner')
merged_mention_list = mentiondetection.clean_ner_result(ner_result_file)
merged_mention_list.sort(key=lambda x: x.span[0])
wiki_link.link_all(doc_text, merged_mention_list)
for mention in merged_mention_list:
if (not mention.mesh_id) and mention.chebi_id < 0 < mention.wid:
cur_name = doc_text[mention.span[0]:mention.span[1] + 1].lower()
print cur_name, mention.wid, wiki_info.get_info(mention.wid)[0]
print time() - start_time
def test():
start_time = time()
text = 'last opportunities Texas senator Cruz'
word_idf_file = 'e:/el/tmpres/demo/merge/word_idf.txt'
tfidf = TfIdf(word_idf_file)
wiki_info_file = 'e:/el/tmpres/demo/wiki-all/wiki-info.pkl'
links_file = 'e:/el/tmpres/demo/wiki-all/links.txt'
description_file = 'e:/el/tmpres/demo/wiki-all/text.txt'
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
wiki_link = WikiLink('e:/el/tmpres/wiki/dict/name_candidates.pkl', wiki_info, tfidf)
context_tfidf = tfidf.get_tfidf_from_text(text)
print wiki_link.link_with_context('cruz', context_tfidf)
print time() - start_time
def test():
start_time = time()
text = 'last opportunities Texas senator Cruz'
word_idf_file = 'e:/el/tmpres/demo/merge/word_idf.txt'
tfidf = TfIdf(word_idf_file)
wiki_info_file = 'e:/el/tmpres/demo/wiki-all/wiki-info.pkl'
links_file = 'e:/el/tmpres/demo/wiki-all/links.txt'
description_file = 'e:/el/tmpres/demo/wiki-all/text.txt'
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
wiki_link = WikiLink('e:/el/tmpres/wiki/dict/name_candidates.pkl',
wiki_info, tfidf)
context_tfidf = tfidf.get_tfidf_from_text(text)
print wiki_link.link_with_context('cruz', context_tfidf)
print time() - start_time
def init_model():
# extra_wiki_desc_file = 'e:/el/tmpres/demo/merge/wiki_extra_sentences.txt'
# extra_parents_file = 'e:/el/tmpres/demo/extra_parents.txt'
#
# name_wid_file = 'e:/el/tmpres/demo/dict/single_candidates_wid_dict.txt'
# record_file = 'd:/data/lab_demo/med_edl_data/records_info_with_wiki.txt'
# dict_file = 'd:/data/lab_demo/med_edl_data/med_dict_ascii_with_ids_edited.txt'
# tree_number_file = 'd:/data/lab_demo/med_edl_data/id_tn.txt'
# res_dir = '/media/dhl/Data/el/tmpres/demo/del-data/'
# input_file = '/media/dhl/Data/el/tmpres/NER/NER/00000001.txt.bak'
# output_file = '/media/dhl/Data/el/tmpres/demo/result/result-linux.json'
res_dir = 'e:/data/el/tmpres/demo/del-data/'
extra_wiki_desc_file = res_dir + 'wiki_extra_sentences.txt'
extra_parents_file = res_dir + 'extra_parents.txt'
mesh_record_file = res_dir + 'records_info_with_wiki.txt'
mesh_dict_file = res_dir + 'med_dict_ascii_with_ids_edited.txt'
exclude_words_file = res_dir + 'exclude_words.txt'
tree_number_file = res_dir + 'id_tn.txt'
obo_file = res_dir + 'chebi.obo'
word_idf_file = 'e:/data/el/tmpres/demo/word_idf.txt'
# wiki_candidates_file = 'e:/el/tmpres/wiki/dict/name_candidates.txt'
wiki_candidates_file = 'e:/data/el/tmpres/wiki/dict/name_candidates.pkl'
# wiki_info_file = r'E:\el\tmpres\demo\wiki-med\new\wiki-info.txt'
# links_file = r'E:\el\tmpres\demo\wiki-med\new\links.txt'
# description_file = r'E:\el\tmpres\demo\wiki-med\new\text.txt'
wiki_info_file = 'e:/data/el/tmpres/demo/wiki-all/wiki-info.pkl'
links_file = 'e:/data/el/tmpres/demo/wiki-all/links.txt'
description_file = 'e:/data/el/tmpres/demo/wiki-all/text.txt'
mesh_extra_description_file = 'e:/data/el/tmpres/demo/extra_description_for_mesh.txt'
chebi_terms = ChebiTerm.load_obo_file(obo_file)
print '%d chebi terms' % len(chebi_terms)
mesh_match = MeshMatch(mesh_dict_file, exclude_words_file)
mesh_records = MeshRecord.load_mesh_records(mesh_record_file)
mesh_tree = MeshTree(tree_number_file, mesh_records)
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
tfidf = TfIdf(word_idf_file)
wiki_link = WikiLink(wiki_candidates_file, wiki_info, tfidf)
extra_wiki_desc = ioutils.load_wiki_extra_descriptions(
mesh_extra_description_file)
# extra_wiki_desc = ioutils.load_wiki_extra_sentences(extra_wiki_desc_file)
med_link = MedLink(extra_parents_file, mesh_match, mesh_records, mesh_tree,
chebi_terms, wiki_info, extra_wiki_desc, wiki_link)
return med_link
def init_model():
res_dir = 'e:/data/el/tmpres/'
# res_dir = '/home/dhl/data/el/tmpres/'
del_res_dir = os.path.join(res_dir, 'demo/del-data/')
# extra_wiki_desc_file = del_res_dir + 'wiki_extra_sentences.txt'
# extra_parents_file = del_res_dir + 'extra_parents.txt'
# mesh_record_file = del_res_dir + 'records_info_with_wiki.txt'
# mesh_dict_file = del_res_dir + 'med_dict_ascii_with_ids_edited.txt'
# exclude_words_file = del_res_dir + 'exclude_words.txt'
# tree_number_file = del_res_dir + 'id_tn.txt'
# obo_file = del_res_dir + 'chebi.obo'
extra_wiki_desc_file = os.path.join(del_res_dir,
'wiki_extra_sentences.txt')
extra_parents_file = os.path.join(del_res_dir, 'extra_parents.txt')
mesh_record_file = os.path.join(del_res_dir, 'records_info_with_wiki.txt')
mesh_dict_file = os.path.join(del_res_dir,
'med_dict_ascii_with_ids_edited.txt')
exclude_words_file = os.path.join(del_res_dir, 'exclude_words.txt')
tree_number_file = os.path.join(del_res_dir, 'id_tn.txt')
obo_file = os.path.join(del_res_dir, 'chebi.obo')
word_idf_file = os.path.join(res_dir, 'demo/word_idf.txt')
wiki_candidates_file = os.path.join(res_dir,
'wiki/dict/name_candidates.pkl')
wiki_info_file = os.path.join(res_dir, 'demo/wiki-all/wiki-info.pkl')
links_file = os.path.join(res_dir, 'demo/wiki-all/links.txt')
description_file = os.path.join(res_dir, 'demo/wiki-all/text.txt')
mesh_extra_description_file = os.path.join(
res_dir, 'demo/extra_description_for_mesh.txt')
# wiki_candidates_file = 'e:/el/tmpres/wiki/dict/name_candidates.txt'
# wiki_candidates_file = 'e:/data/el/tmpres/wiki/dict/name_candidates.pkl'
# wiki_info_file = 'e:/data/el/tmpres/demo/wiki-all/wiki-info.pkl'
# links_file = 'e:/data/el/tmpres/demo/wiki-all/links.txt'
# description_file = 'e:/data/el/tmpres/demo/wiki-all/text.txt'
# mesh_extra_description_file = 'e:/data/el/tmpres/demo/extra_description_for_mesh.txt'
chebi_terms = ChebiTerm.load_obo_file(obo_file)
mesh_match = MeshMatch(mesh_dict_file, exclude_words_file)
mesh_records = MeshRecord.load_mesh_records(mesh_record_file)
mesh_tree = MeshTree(tree_number_file, mesh_records)
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
tfidf = TfIdf(word_idf_file)
wiki_link = WikiLink(wiki_candidates_file, wiki_info, tfidf)
extra_wiki_desc = ioutils.load_wiki_extra_descriptions(
mesh_extra_description_file)
# extra_wiki_desc = ioutils.load_wiki_extra_sentences(extra_wiki_desc_file)
tmp_med_link = MedLink(extra_parents_file, mesh_match, mesh_records,
mesh_tree, chebi_terms, wiki_info, extra_wiki_desc,
wiki_link)
return tmp_med_link
def __init_mellink():
word_idf_file = 'e:/data/el/tmpres/demo/word_idf.txt'
wiki_candidates_file = 'e:/data/el/tmpres/wiki/dict/name_candidates.pkl'
wiki_info_file = 'e:/data/el/tmpres/demo/wiki-all/wiki-info.pkl'
links_file = 'e:/data/el/tmpres/demo/wiki-all/links.txt'
description_file = 'e:/data/el/tmpres/demo/wiki-all/text.txt'
wiki_info = WikiInfo(wiki_info_file, links_file, description_file)
tfidf = TfIdf(word_idf_file)
wiki_link = WikiLink(wiki_candidates_file, wiki_info, tfidf)
return MedLink(wiki_info=wiki_info, wiki_link=wiki_link)
def wiki_merge(self, push_to_wiki=False, lifetime=False, overwrite_wiki=False):
"""
Merge local collection with table on wiki
"""
pagename=None
if not lifetime:
pagename=self._get_filename(nameonly=True)
else:
pagename='livstidsmedlemmer_fra_script'
self.wl=WikiLink(pagename=pagename)
ok, msg=self.wl.login()
if not ok:
return{u'status':u'Failure while accessing wiki. error: {}'.format(msg)}
val={}
if overwrite_wiki:
self.wl.clear_page()
val['pre']='== Medlemsliste ==\n'
val['post']=''
else:
ok, val=self._merge()
if not ok:
return val
if push_to_wiki:
ok, table=self.wl.dict_to_table(self.storage, ['id', 'name', 'date', 'lifetime'], lifetime=lifetime)
if not ok:
return {u'status':table}
text=u'{}{}{}'.format(val['pre'], table, val['post'])
if overwrite_wiki:
summary='Overwritten from script'
else:
summary='Merge from script'
self.wl.write(text=text, summary=summary)
return {u'status':u'Merged local storage with wiki and updated changes on wiki'}
return {u'status':u'wiki merged with local storage'}
class Storage:
"""
A simple class used to save data, and back it up.
TODO: add sync to our `wiki`_. - Update! Almost done!
.. _wiki: http://wiki.cyb.no
"""
def __init__(self, **kwargs):
"""
Constructor. Takes a python-dict `kwargs` as argument. kwargs must contain
a list/dict `fields` where all values in `fields` will be required to create
new objects and a single value `ident` used to fetch a specific object instead of an `id`.
if kwargs contains boolean 'uniqueident' and it is set to True, then 'ident' must be unique
on create.
:param \*\*kwargs: dict containing valid fields for an object, and ident-field.
"""
self.storage={}
self.uniqueident=False
self.objectname='Object'
if 'fields' in kwargs:
self.fields=kwargs['fields']
if 'ident' in kwargs:
self.ident=kwargs['ident']
if 'uniqueident' in kwargs:
self.uniqueident=kwargs['uniqueident']
if 'objectname' in kwargs:
self.objectname=kwargs['objectname']
if 'gui' in kwargs:
self.gui=kwargs['gui']
self.wks=None
self.wl=None
self.filename=self._get_filename()
def create(self, **kwargs):
"""
Adds an object to collection with values from `kwargs`. If `self.fields` is used, only
values from `fields` will be used, and all values from `fields` are required.
All objects will automatically be given an `id` using :func:`_unique_id()<storage.Storage._unique_id>`.
:param \*\*kwargs: dict with all fields for a new object.
:returns: a dict with either 'success' containing the new object, or 'error' with errormessage.
"""
if 'name' in kwargs:
name=kwargs['name'].strip()
if len(name.split())<2:
return {u'error':u'You have to enter a full name!'}
if len(name)<5:
return {u'error':u'A name has to be more than 5 letters'}
if self.uniqueident:
if 'success' in self.read(**{self.ident:kwargs[self.ident]}):
return {u'error':u'{} with {} {} already exists!'.format(self.objectname, self.ident, kwargs[self.ident])}
args={}
for f in self.fields:
if not f in kwargs:
return {u'error':u'missing field {} in arguments!'.format(f)}
if kwargs[f]=='':
return {u'error':u'missing value for field: {}!'.format(f)}
value=u'{}'.format(kwargs[f]).strip().lower()
args[f]=value#unicode(kwargs[f])
key=self._unique_id()
self.storage[key]=args
return {u'success':key, 'object':args}
def read(self, **kwargs):
"""
Find and return a spesific object from storage. Either based on `id` or `self.ident`
:param kwargs: dict containing either `id` or `self.ident`
:returns: a dict with either 'success' containing the object, or 'error' with errormessage.
"""
if len(self.storage)==0:
return {u'error':u'empty collection'}
if 'id' in kwargs:
if kwargs['id'] in self.storage:
return {u'success':self.storage[kwargs['id']]}
match=0
if self.ident in kwargs:
for k, v in self.storage.iteritems():
if v[self.ident]:
if v[self.ident]==kwargs[self.ident]:
retval=v
match+=1
if match>1:
return {u'error':u'multiple {}s matching name'.format(self.objectname)}
if match==1:
return {u'success':retval}
return {u'error':u'no {}s found'.format(self.objectname)}
def update(self, **kwargs):
"""
find an element based on `id` and update with values in `kwargs`. Any values in kwargs that
are not in self.fields are ignored.
:param kwargs: dict containing `id` of object as well as updated fields.
:returns: a dict with either 'success' containing the updated object, or 'error' with errormessage.
"""
if len(self.storage)==0:
return {u'error':u'empty collection'}
if not 'id' in kwargs:
return {u'error':u'No id provided'}
if not kwargs['id'] in self.storage:
return {u'error':u'Provided id does not exist'}
if 'life' in kwargs:
if kwargs['life']:
return self._set_lifetime(kwargs['id'])
else:
return self._unset_lifetime(kwargs['id'])
id=kwargs['id']
del kwargs['id']
obj=self.storage[id]
for k, v in kwargs.iteritems():
if k in self.fields:
obj[k]=v
return {u'success':self.storage[id]}
def delete(self, **kwargs):
"""
finds and deletes an object based on `id`
:param kwargs: dict containing id of object.
:returns: a dict with either 'success' containing the deleted `id`, or 'error' with errormessage.
"""
if len(self.storage)==0:
return {u'error':u'empty collection'}
if not 'id' in kwargs:
return {u'error':u'No id provided'}
if not kwargs['id'] in self.storage:
return {u'error':u'No {} matching id: {}'.format(self.objectname, kwargs['id'])}
del self.storage[kwargs['id']]
return {u'success':u'{} with id {} is deleted'.format(self.objectname, kwargs['id'])}
def search(self, **kwargs):
"""
search for any object that contains any values from `kwargs`.
:param kwargs: dict containing search-fields. any field not in self.fields are ignored.
:retval: returns a dictionary containing all objects that match search-fields.
"""
retval={}
for k, v in self.storage.iteritems():
match=False
for ak, av in kwargs.iteritems():
if not match and ak in self.fields and not av=='':
value=v[ak]
if av in value:
retval[k]=v
match=True
return retval
def _set_lifetime(self, id):
"""
Set a user as lifetime member.
Give the user a lifetime ID: Lx where x is number.
"""
if self.storage[id]['lifetime']=='y':
return {u'error':u'{} already has a lifetime membership'.format(self.storage[id]['name'].title())}
lid=self._unique_id(True)
self.storage[lid]=self.storage[id]
self.storage[lid]['lifetime']='y'
del self.storage[id]
return {u'success':u'{} now has id {} and a lifetime membership'.format(self.storage[lid]['name'].title(), lid)}
def _unset_lifetime(self, lid):
"""
Unset lifetime flag from a user.
Give the user a normal id, instead of lifetime id.
"""
if self.storage[lid]['lifetime']=='n':
return {u'error':u'{} does not have a lifetime membership'.format(self.storage[id]['name'].title())}
id=self._unique_id()
self.storage[id]=self.storage[lid]
self.storage[id]['lifetime']='n'
del self.storage[lid]
return {u'success':u'{} now has id {}, and have lost the lifetime membership'.format(self.storage[id]['name'].title(), id)}
def update_id(self, oldid, newid):
"""
Change/update the id of a person.
"""
tmp=self.storage[oldid]
if tmp['lifetime']=='y':
if not 'L' in newid:
newid='L{}'.format(newid)
if newid in self.storage:
return {'status':'FAILURE: Chosen id is already in use.'}
self.storage[newid]=tmp
del self.storage[oldid]
return {'status':'Success! Updated the users id!'}
def _unique_id(self, life=False):
"""
Finds the first availible id and returns it.
:returns: the first availible id.
"""
if life:
i=0
val='L0'
while val in self.storage:
i+=1
val='L{}'.format(i)
return val
i=0
while i in self.storage:
i+=1
return i
def save(self):
"""
Saves entire collection to file. Filename is provided by :func:`_get_filename<storage.Storage._get_filename>`
The collection is stored as JSON.
"""
try:
f=open(self.filename, 'w')
js=json.dumps(self.storage, indent=3, sort_keys=True)
f.write(js)
f.close()
except:
return {'msg':'Could not write to file!', 'status':False}
return {'msg':'Storage written to file.', 'status':True}
def load(self):
"""
Load from file if file exists. Filename is provided by :func:`_get_filename<storage.Storage._get_filename>`
This function assumes that the collection is stored as JSON, created by :func:`save<storage.Storage.save>`.
"""
js=''
if os.path.exists(self.filename):
f=open(self.filename, 'r')
js=f.read()
f.close()
if js=='' or js=='{}':
retval=self._load_lifetime()
if 'success' in retval:
retval['success']='No current file found. {}'.format(retval['success'])
elif 'error' in retval:
retval['error']='No current file found. {}'.format(retval['error'])
return retval
#bugfix for keys..
tmp=json.loads(js)
for k, v in tmp.iteritems():
if not 'L' in k:
self.storage[int(k)]=v
else:
self.storage[k]=v
return {u'success':u'Loaded all data from file'}
def _load_lifetime(self):
"""
load lifetime-members from past periods. gets the filename for the current period and adds
all lifetime-members from the last period to storage.
:param filename: the filename of the current period.
"""
m=re.search('(.+)medlemmer_(\S)(\d\d)\.json', self.filename)
path=m.group(1)
s=m.group(2)
y=m.group(3)
old_fname=''
if s=='h':
old_fname='{}medlemmer_{}{}.json'.format(path, 'v', y)
elif s=='v':
old_fname='{}medlemmer_{}{}.json'.format(path, 'h', (y-1))
if not os.path.exists(old_fname):
return {u'error':u'Previous file could not be found, no lifetime members loaded.'}
f=open(old_fname, 'r')
old_storage=json.loads(f.read())
for k, v in old_storage.iteritems():
if 'L' in k and v['lifetime']=='y':
self.storage[k]=v
return {u'success':u'loaded all lifetime members from previous file'}
def _get_filename(self, nameonly=False):
"""
Calculates and returns current filename, e.g. 'medlemmer_h12' for autumn 2012.
:returns: current filename.
"""
month=dt.now().strftime("%m")
year=dt.now().strftime("%y")
path=os.path.abspath(__file__).rsplit('/', 1)[0]
if month<8:
if nameonly:
return 'medlemmer_v{}'.format(year)
return '{}/medlemslister/medlemmer_v{}.json'.format(path, year)
if nameonly:
return 'medlemmer_h{}'.format(year)
return '{}/medlemslister/medlemmer_h{}.json'.format(path, year)
def size(self):
"""
returns the size of the collection
"""
return len(self.storage)
def _testfile(self):
try:
open(self.filename, 'a')
except(IOError):
return False
return True
def google_write(self):
"""
backup collection to a google spreadsheet.
Note: lazy backup, does not merge.. overwrites google-data.
"""
if not self._get_google_sheet():
return {u'error':u'could not connect to google spreadsheet'}
try:
val=self.wks.col_values(1)
except ValueError:
val=[]
for i in xrange(1, len(val)+1):
self.wks.update_cell(i, 1, '')
self.wks.update_cell(i, 2, '')
x=1
for k, v in self.storage.iteritems():
self.wks.update_cell(x, 1, '{}'.format(k))
self.wks.update_cell(x, 2, json.dumps(v))
x+=1
return {u'success':u'backed up to google'}
def google_read(self):
"""
read backup of collection from a google spreadsheet, merge values based on id and date.
"""
if not self._get_google_sheet():
return {u'error':u'could not connect to google spreadsheet'}
empty=False
try:
keys=self.wks.col_values(1)
vals=self.wks.col_values(2)
except ValueError:
empty=True
if empty:
return {u'error':u'spreadsheet is empty!'}
gdoc={}
for i in xrange(0, len(keys)):
gdoc[keys[i]]=json.loads(vals[i])
for k, v in gdoc.iteritems():
if not k in self.storage:
self.storage[k]=v
else:
if v['date']>self.storage[k]['date']:
self.storage[k]=v
return {u'success':u'read and merged all values from google doc.'}
def wiki_merge(self, push_to_wiki=False, lifetime=False, overwrite_wiki=False):
"""
Merge local collection with table on wiki
"""
pagename=None
if not lifetime:
pagename=self._get_filename(nameonly=True)
else:
pagename='livstidsmedlemmer_fra_script'
self.wl=WikiLink(pagename=pagename)
ok, msg=self.wl.login()
if not ok:
return{u'status':u'Failure while accessing wiki. error: {}'.format(msg)}
val={}
if overwrite_wiki:
self.wl.clear_page()
val['pre']='== Medlemsliste ==\n'
val['post']=''
else:
ok, val=self._merge()
if not ok:
return val
if push_to_wiki:
ok, table=self.wl.dict_to_table(self.storage, ['id', 'name', 'date', 'lifetime'], lifetime=lifetime)
if not ok:
return {u'status':table}
text=u'{}{}{}'.format(val['pre'], table, val['post'])
if overwrite_wiki:
summary='Overwritten from script'
else:
summary='Merge from script'
self.wl.write(text=text, summary=summary)
return {u'status':u'Merged local storage with wiki and updated changes on wiki'}
return {u'status':u'wiki merged with local storage'}
def _merge(self):
ok, msg=self.wl.read()
if not ok:
return{u'status':u'Failure while accessing wiki. error: {}'.format(msg)}
wiki=self.wl.wikitable_to_dict()
ok, values=wiki['dict']
if not ok:
return false, {u'status':values}
tmp=self.storage
for wk, wv in values.iteritems():
if wk in tmp:
sv=tmp[wk]
if wv['name'].strip()!=sv['name'].strip():
return {u'status':u'Failure while merging. Conflict! {} in wiki and {} in local storage have the same id! Please inform sys-admin.'.format(wv['name'], sv['name'])}
else:
match=False
for sk, sv in tmp.iteritems():
if v['name']==sv['name']:
match=True
if match:
return {u'status':u'Failure while merging. Conflict! {} is in wiki and local storage with different ids! Please inform sys-admin.'.format(v['name'])}
tmp[k]=v
self.storage=tmp
return True, values
def _get_google_sheet(self):
"""
Connect to a google spreadsheet
:returns: True if success, False if not
"""
if self.wks:
return True
name=self._get_filename(nameonly=True)
gc=gspread.login(username, passwd)
try:
wks=gc.open(name).sheet1
except SpreadsheetNotFound:
return False
self.wks=wks
return True
