def _expected_norm_array_name(self):
"""Returns the name that an accumulation array should have, if it
exists in the file system. This is based on the original filename and
a hash of the transformation matrix."""
transform_string=''.join([struct.pack('<d', x)
for x in self.transform])
the_hash=hashlib.md5(transform_string).hexdigest()
return os.path.join(cache.path(),
'%s.%s' % (os.path.basename(self._matrix_file.name),
the_hash))
def _expected_norm_array_name(self):
"""Returns the name that an accumulation array should have, if it
exists in the file system. This is based on the original filename and
a hash of the transformation matrix."""
transform_string = ''.join(
[struct.pack('<d', x) for x in self.transform])
the_hash = hashlib.md5(transform_string).hexdigest()
return os.path.join(
cache.path(),
'%s.%s' % (os.path.basename(self._matrix_file.name), the_hash))
import sys
import os
import web
import cPickle as pickle
import traceback
import urllib2
from urllib import urlencode
from MEDRank.file.disk_backed_dict import StringDBDict, DatabaseError
from MEDRank.utility.logger import logging, ULTRADEBUG
from MEDRank.utility import cache
from Bio import (Entrez, Medline)
urls = ("/(\d+)", "PubmedRecord")
app = web.application(urls, globals())
DEFAULT_CACHE_NAME = os.path.join(cache.path(), "pubmed_cache.db")
DEFAULT_CACHE_PORT = 8081
DEFAULT_CACHE_HOST = "http://127.0.0.1:%d" % DEFAULT_CACHE_PORT
# Replace your email address below!
Entrez.email = "*****@*****.**"
class PubmedRecord(object):
"""Serves PubMed records via a RESTful API"""
def __init__(self):
try:
self._cache_location = sys.argv[2]
except IndexError:
self._cache_location = DEFAULT_CACHE_NAME
self._cache = StringDBDict(self._cache_location, file_mode="c")
# encoding: utf-8
"""
infer_relation_direction.py
Uses MRREL to infer a relation's directionality, given two CUIs.
Created by Jorge Herskovic on 2008-06-24.
Copyright (c) 2008 Jorge Herskovic. All rights reserved.
"""
import os.path
import operator
import sys
from MEDRank.utility import cache
from MEDRank.utility.logger import logging, ULTRADEBUG
#from MEDRank.file.mrrel import (MRRELTable, MRRELLine)
_DEFAULT_FILE_NAME=os.path.join(cache.path(),
"direction_inference.p.bz2")
class RelationDirectionInferrer(dict):
def build_from_mrrel_file_and_stype_table(self, mrrel_table,
semantic_types):
"""Builds a relationship dictionary and stores a semantic type
table."""
count=0
self._stypes=semantic_types
for l in mrrel_table:
if l.original_direction:
if l.cui1==l.cui2: # Relationships of a concept to itself are
# not interesting to us.
continue
import sys
import os
import web
import cPickle as pickle
import traceback
import urllib2
from urllib import urlencode
from MEDRank.file.disk_backed_dict import StringDBDict, DatabaseError
from MEDRank.utility.logger import logging, ULTRADEBUG
from MEDRank.utility import cache
from Bio import (Entrez, Medline)
urls=("/(\d+)", "PubmedRecord")
app = web.application(urls, globals())
DEFAULT_CACHE_NAME=os.path.join(cache.path(), "pubmed_cache.db")
DEFAULT_CACHE_PORT=8081
DEFAULT_CACHE_HOST="http://127.0.0.1:%d" % DEFAULT_CACHE_PORT
# Replace your email address below!
Entrez.email="*****@*****.**"
class PubmedRecord(object):
"""Serves PubMed records via a RESTful API"""
def __init__(self):
try:
self._cache_location=sys.argv[2]
except IndexError:
self._cache_location=DEFAULT_CACHE_NAME
self._cache=StringDBDict(self._cache_location, file_mode="c")
current_element = None
current_article = None
current_cuis = None
current_names = None
current_nodes = None
current_relations = None
current_strengths = None
current_links = None
current_content = []
article_handler = re.compile(r"\<\s*article\s*pmid\s*\=\s*(\w+)\s*\>",
re.IGNORECASE)
known_opening_tags = re.compile(r"\<(cuis|names|connectivities|relations)\>",
re.IGNORECASE)
known_closing_tags = re.compile(r"\</(cuis|names|connectivities|relations)\>",
re.IGNORECASE)
SEMPRED_CACHE = os.path.join(cache.path(), "sempred")
def predication_filename(pubmed_id):
p = list(str(pubmed_id))
p, last_two = p[:-2], p[-2:]
ptuple = tuple(['_%s' % x for x in p])
if ptuple == ():
fn = ''.join(last_two)
else:
fn = os.path.join(os.path.join(*ptuple), ''.join(last_two))
logging.debug("Predication filename for %r=%s", pubmed_id, fn)
return fn
def predications_name_and_path(pubmed_id, path):
current_element=None
current_article=None
current_cuis=None
current_names=None
current_nodes=None
current_relations=None
current_strengths=None
current_links=None
current_content=[]
article_handler=re.compile(r"\<\s*article\s*pmid\s*\=\s*(\w+)\s*\>",
re.IGNORECASE)
known_opening_tags=re.compile(r"\<(cuis|names|connectivities|relations)\>",
re.IGNORECASE)
known_closing_tags=re.compile(r"\</(cuis|names|connectivities|relations)\>",
re.IGNORECASE)
SEMPRED_CACHE=os.path.join(cache.path(), "sempred")
def predication_filename(pubmed_id):
p=list(str(pubmed_id))
p, last_two=p[:-2], p[-2:]
ptuple=tuple(['_%s' % x for x in p])
if ptuple==():
fn=''.join(last_two)
else:
fn=os.path.join(os.path.join(*ptuple), ''.join(last_two))
logging.debug("Predication filename for %r=%s", pubmed_id, fn)
return fn
def predications_name_and_path(pubmed_id, path):
filename=os.path.join(path, "%s.pickle.bz2" %
predication_filename(pubmed_id))