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))