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Commit 9eead9fa authored by delanoe's avatar delanoe
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[FEAT] Scrapper pubmed: ok

parent 88036658
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Showing with 269 additions and 262 deletions
gargantext/constants.py
View file @ 9eead9fa
......@@ -47,59 +47,59 @@ def convert_to_date(date):
return dateutil.parser.parse(date)
INDEXED_HYPERDATA = {
# TODO use properties during toolchain.hyperdata_indexing
# TODO use properties during toolchain.hyperdata_indexing
# (type, convert_to_db, convert_from_db)
'count':
{ 'id' : 1
, 'type' : int
, 'convert_to_db' : int
, 'convert_from_db': int
},
'publication_date':
{ 'id' : 2
, 'type' : datetime.datetime
, 'convert_to_db' : convert_to_date
, 'convert_from_db': datetime.datetime.fromtimestamp
},
'title':
{ 'id' : 3
, 'type' : str
, 'convert_to_db' : str
, 'convert_from_db': str
},
'authors':
{ 'id' : 4
, 'type' : str
, 'convert_to_db' : str
, 'convert_from_db': str
},
'journal':
{ 'id' : 5
, 'type' : str
, 'convert_to_db' : str
, 'convert_from_db': str
},
'abstract':
{ 'id' : 6
, 'type' : str
, 'convert_to_db' : str
, 'convert_from_db': str
},
'text':
{ 'id' : 7
, 'type' : str
, 'convert_to_db' : str
, 'convert_from_db': str
},
'page':
{ 'id' : 8
, 'type' : int
......
gargantext/util/files.py
View file @ 9eead9fa
from gargantext.constants import *
from gargantext.constants import *
from gargantext.util.digest import str_digest
from gargantext.util import http
from gargantext.util import http
def save(contents, name='', basedir=''):
......
gargantext/util/http.py
View file @ 9eead9fa
......@@ -29,7 +29,7 @@ import urllib.request
def get(url):
response = urllib.request.urlopen(url)
html = response.read()
return response.read()
# retrieve GET parameters from a request
......
gargantext/views/pages/projects.py
View file @ 9eead9fa
......@@ -94,7 +94,7 @@ def project(request, project_id):
)
session.add(corpus)
session.commit()
# parse_extract: fileparsing -> ngram extraction -> lists
scheduled(parse_extract_indexhyperdata)(corpus.id)
......
scrapers/MedlineFetcher.py
View file @ 9eead9fa
......@@ -2,10 +2,15 @@
# ***** Medline Fetcher *****
# ****************************
# MEDLINE USER REQUIREMENT : Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays
# MEDLINE USER REQUIREMENT : Run retrieval scripts on weekends or
# between 9 pm and 5 am Eastern Time weekdays
from gargantext.util.files import download
import sys
if sys.version_info >= (3, 0): from urllib.request import urlopen
else: from urllib import urlopen
import os
import time
# import libxml2
......@@ -21,48 +26,60 @@ from queue import Queue
class MedlineFetcher:
def __init__(self):
self.queue_size = 8
self.q = Queue()
self.firstResults = []
self.lock = threading.Lock() # lock to serialize console output
self.queue_size = 8
self.q = Queue()
self.firstResults = []
self.lock = threading.Lock() # lock to serialize console output
self.pubMedEutilsURL = 'http://www.ncbi.nlm.nih.gov/entrez/eutils'
self.pubMedDB = 'Pubmed'
self.reportType = 'medline'
self.pubMedDB = 'Pubmed'
self.reportType = 'medline'
# Return the globalResults!:
# - count =
# - queryKey =
# - webEnv =
# - count =
# - queryKey =
# - webEnv =
def medlineEsearch(self , query):
# print ("MedlineFetcher::medlineEsearch :")
"Get number of results for query 'query' in variable 'count'"
"Get also 'queryKey' and 'webEnv', which are used by function 'medlineEfetch'"
# print(query)
origQuery = query
query = query.replace(' ', '%20')
eSearch = '%s/esearch.fcgi?db=%s&retmax=1&usehistory=y&term=%s' %(self.pubMedEutilsURL, self.pubMedDB, query)
query = query.replace(' ', '%20')
eSearch = '%s/esearch.fcgi?db=%s&retmax=1&usehistory=y&term=%s' \
% ( self.pubMedEutilsURL, self.pubMedDB, query )
try:
eSearchResult = urlopen(eSearch)
data = eSearchResult.read()
root = etree.XML(data)
findcount = etree.XPath("/eSearchResult/Count/text()")
count = findcount(root)[0]
findquerykey = etree.XPath("/eSearchResult/QueryKey/text()")
queryKey = findquerykey(root)[0]
findwebenv = etree.XPath("/eSearchResult/WebEnv/text()")
webEnv = findwebenv(root)[0]
except:
count=0
queryKey=False
webEnv=False
origQuery=False
values = { "query":origQuery , "count": int(str(count)), "queryKey": queryKey , "webEnv":webEnv }
data = eSearchResult.read()
root = etree.XML(data)
findcount = etree.XPath("/eSearchResult/Count/text()")
count = findcount(root)[0]
findquerykey = etree.XPath("/eSearchResult/QueryKey/text()")
queryKey = findquerykey(root)[0]
findwebenv = etree.XPath("/eSearchResult/WebEnv/text()")
webEnv = findwebenv(root)[0]
except Exception as Error:
print(Error)
count = 0
queryKey = False
webEnv = False
origQuery = False
values = { "query" : origQuery
, "count" : int(count)
, "queryKey" : queryKey
, "webEnv" : webEnv
}
return values
......@@ -70,52 +87,32 @@ class MedlineFetcher:
# Total number of UIDs from the retrieved set to be shown in the XML output (default=20)
# maximum of 100,000 records
def medlineEfetchRAW( self , fullquery):
query = fullquery["string"]
retmax = fullquery["retmax"]
count = fullquery["count"]
queryKey = fullquery["queryKey"]
webEnv = fullquery["webEnv"]
query = fullquery [ "string" ]
retmax = fullquery [ "retmax" ]
count = fullquery [ "count" ]
queryKey = fullquery [ "queryKey"]
webEnv = fullquery [ "webEnv" ]
"Fetch medline result for query 'query', saving results to file every 'retmax' articles"
queryNoSpace = query.replace(' ', '') # No space in directory and file names, avoids stupid errors
# print ("LOG::TIME: ",'medlineEfetchRAW :Query "' , query , '"\t:\t' , count , ' results')
retstart = 0
eFetch = '%s/efetch.fcgi?email=youremail@example.org&rettype=%s&retmode=xml&retstart=%s&retmax=%s&db=%s&query_key=%s&WebEnv=%s' %(self.pubMedEutilsURL, self.reportType, retstart, retmax, self.pubMedDB, queryKey, webEnv)
return eFetch
def ensure_dir(self , f):
d = os.path.dirname(f)
if not os.path.exists(d):
os.makedirs(d)
# generic!
def downloadFile(self, item):
url = item[0]
filename = item[1]
# print("\tin test_downloadFile:")
# print(url,filename)
data = urlopen(url)
f = codecs.open(filename, "w" ,encoding='utf-8')
myfile = File(f)
myfile.write( data.read().decode('utf-8') )
myfile.close()
f.close()
def download(self, url):
print(url)
filename = download(url)
with self.lock:
print(threading.current_thread().name, filename+" OK")
return filename
# generic!
def test_downloadFile(self, item):
url = item[0]
filename = item[1]
# print("\tin downloadFile:")
data = urlopen(url)
return data
# generic!
def do_work(self,item):
......@@ -132,23 +129,24 @@ class MedlineFetcher:
self.firstResults.append(self.do_work(item))
self.q.task_done()
def worker2(self):
while True:
item = self.q.get()
results = []
try: result = self.downloadFile(item)
except: result = False
try:
result = self.download(item)
except Exception as error :
print(error)
result = False
self.firstResults.append(result)
self.q.task_done()
def chunks(self , l , n):
print("chunks:")
for i in range(0, len(l), n):
yield l[i:i+n]
# GLOBALLIMIT:
# I will retrieve this exact amount of publications.
# The publications per year i'll retrieve per year will be = (k/N)*GlobalLimit <- i'll use this as RETMAX
# The publications per year i'll retrieve per year will be :
# (k/N)*GlobalLimit
# \_ this is used as RETMAX
# - k : Number of publications of x year (according to pubmed)
# - N : Sum of every k belonging to {X} (total number of pubs according to pubmed)
# - GlobalLimit : Number of publications i want.
......@@ -172,7 +170,7 @@ class MedlineFetcher:
# print ('---------\n')
pubmedquery = str(year) + '[dp] '+query
self.q.put( pubmedquery ) #put task in the queue
self.q.join()
print('time:',time.perf_counter() - start)
......@@ -183,15 +181,16 @@ class MedlineFetcher:
Total += 1
if globalresults["queryKey"]==False:
Fails += 1
if globalresults["count"]>0:
if globalresults["count"] > 0 :
N+=globalresults["count"]
queryhyperdata = {
"string": globalresults["query"] ,
"count": globalresults["count"] ,
"queryKey":globalresults["queryKey"] ,
"webEnv":globalresults["webEnv"] ,
"retmax":0
}
queryhyperdata = { "string" : globalresults["query"]
, "count" : globalresults["count"]
, "queryKey" : globalresults["queryKey"]
, "webEnv" : globalresults["webEnv"]
, "retmax" : 0
}
thequeries.append ( queryhyperdata )
print("Total Number:", N,"publications")
......@@ -199,14 +198,16 @@ class MedlineFetcher:
print("---------------------------------------\n")
for i,query in enumerate(thequeries):
k = query["count"]
proportion = k/float(N)
k = query["count"]
proportion = k/float(N)
retmax_forthisyear = int(round(globalLimit*proportion))
query["retmax"] = retmax_forthisyear
if query["retmax"]==0: query["retmax"]+=1
query["retmax"] = retmax_forthisyear
if query["retmax"] == 0 : query["retmax"]+=1
print(query["string"],"\t[",k,">",query["retmax"],"]")
if ((Fails+1)/(Total+1))==1 : # for identifying the epic fail or connection error
if ((Fails+1)/(Total+1)) == 1 : # for identifying the epic fail or connection error
thequeries = [False]
return thequeries
scrapers/istex.py 0 → 100644
View file @ 9eead9fa
def getGlobalStatsISTEXT(request ):
"""
ISTEX simply the total of hits for a query
(not reused in testISTEX)
"""
print(request.method)
alist = ["bar","foo"]
if request.method == "POST":
query = request.POST["query"]
N = int(request.POST["N"])
print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" query =", query )
print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" N =", N )
query_string = query.replace(" ","+")
url = "http://api.istex.fr/document/?q="+query_string+"&output=id,title,abstract,pubdate,corpusName,authors,language"
tasks = MedlineFetcher()
try:
thedata_path = tasks.download( url )
thedata = open(thedata_path, "rb")
alist = thedata.read().decode('utf-8')
except Exception as error:
alist = [str(error)]
data = alist
return JsonHttpResponse(data)
def testISTEX(request , project_id):
print("testISTEX:")
print(request.method)
alist = ["bar","foo"]
# implicit global session
# do we have a valid project id?
try:
project_id = int(project_id)
except ValueError:
raise Http404()
# do we have a valid project?
project = (session
.query(Node)
.filter(Node.id == project_id)
.filter(Node.typename == 'PROJECT')
).first()
if project is None:
raise Http404()
# do we have a valid user?
user = request.user
if not user.is_authenticated():
return redirect('/auth/?next=%s' % request.path)
if project.user_id != user.id:
return HttpResponseForbidden()
if request.method == "POST":
query = "-"
query_string = "-"
N = 0
if "query" in request.POST:
query = request.POST["query"]
query_string = query.replace(" ","+") # url encoded q
if "N" in request.POST:
N = int(request.POST["N"]) # query_size from views_opti
if N > QUERY_SIZE_N_MAX:
msg = "Invalid sample size N = %i (max = %i)" % (N, QUERY_SIZE_N_MAX)
print("ERROR (scrap: istex d/l ): ",msg)
raise ValueError(msg)
print("Scrapping Istex: '%s' (%i)" % (query_string , N))
urlreqs = []
pagesize = 50
tasks = MedlineFetcher()
chunks = list(tasks.chunks(range(N), pagesize))
for k in chunks:
if (k[0]+pagesize)>N: pagesize = N-k[0]
urlreqs.append("http://api.istex.fr/document/?q="+query_string+"&output=*&"+"from="+str(k[0])+"&size="+str(pagesize))
resourcetype = RESOURCETYPES["name"]["ISTex"]
# corpus node instanciation as a Django model
corpus = Node(
name = query,
user_id = request.user.id,
parent_id = project_id,
typename = 'CORPUS',
language_id = None,
hyperdata = {'Processing' : "Parsing documents",}
)
session.add(corpus)
session.commit()
corpus_id = corpus.id
print("NEW CORPUS", corpus_id)
ensure_dir(request.user)
tasks = MedlineFetcher()
for i in range(8):
t = threading.Thread(target=tasks.worker2) #thing to do
t.daemon = True # thread dies when main thread (only non-daemon thread) exits.
t.start()
for url in urlreqs:
filename = MEDIA_ROOT + '/corpora/%s/%s' % (request.user, str(datetime.datetime.now().isoformat()))
tasks.q.put( [url , filename]) #put a task in th queue
tasks.q.join() # wait until everything is finished
dwnldsOK = 0
for filename in tasks.firstResults:
if filename!=False:
# add the uploaded resource to the corpus
corpus.add_resource(corpus,
user_id = request.user.id,
type_id = resourcetype.id,
file = filename,
)
dwnldsOK+=1
if dwnldsOK == 0: return JsonHttpResponse(["fail"])
###########################
###########################
try:
scheduled(parse_extract_indexhyperdata(corpus_id,))
except Exception as error:
print('WORKFLOW ERROR')
print(error)
sleep(1)
return HttpResponseRedirect('/project/' + str(project_id))
data = [query_string,query,N]
return JsonHttpResponse(data)
scrapers/pubmed.py
View file @ 9eead9fa
......@@ -8,19 +8,18 @@ import json
import datetime
from os import path
import threading
from gargantext.settings import MEDIA_ROOT, BASE_DIR
#from gargantext.settings import MEDIA_ROOT, BASE_DIR
from django.shortcuts import redirect
from django.http import Http404, HttpResponseRedirect, HttpResponseForbidden
from gargantext.constants import RESOURCETYPES
from gargantext.models.nodes import Node
from gargantext.util.db import session
from gargantext.util.http import JsonHttpResponse
from gargantext.util.tools import ensure_dir
from gargantext.constants import RESOURCETYPES
from gargantext.models.nodes import Node
from gargantext.util.db import session
from gargantext.util.http import JsonHttpResponse
from gargantext.util.tools import ensure_dir
from gargantext.util.scheduling import scheduled
from gargantext.util.toolchain import parse_extract_indexhyperdata
from gargantext.util.toolchain import parse_extract_indexhyperdata
......@@ -37,7 +36,7 @@ QUERY_SIZE_N_MAX = 1000 # int(CONF['scrappers']['QUERY_SIZE_N_MAX'])
# QUERY_SIZE_N_DEFAULT = int(CONF['scrappers']['QUERY_SIZE_N_DEFAULT'])
# --------------------------------------------------------------------
def getGlobalStats(request ):
def getGlobalStats( request ):
"""
Pubmed year by year results
......@@ -73,37 +72,8 @@ def getGlobalStats(request ):
return JsonHttpResponse(data)
def getGlobalStatsISTEXT(request ):
"""
ISTEX simply the total of hits for a query
(not reused in testISTEX)
"""
print(request.method)
alist = ["bar","foo"]
if request.method == "POST":
query = request.POST["query"]
N = int(request.POST["N"])
print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" query =", query )
print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" N =", N )
query_string = query.replace(" ","+")
url = "http://api.istex.fr/document/?q="+query_string+"&output=id,title,abstract,pubdate,corpusName,authors,language"
tasks = MedlineFetcher()
filename = MEDIA_ROOT + '/corpora/%s/%s' % (request.user, str(datetime.datetime.now().isoformat()))
try:
thedata = tasks.test_downloadFile( [url,filename] )
alist = thedata.read().decode('utf-8')
except Exception as error:
alist = [str(error)]
data = alist
return JsonHttpResponse(data)
def doTheQuery(request , project_id):
def doTheQuery( request , project_id ) :
# implicit global session
# do we have a valid project id?
try:
......@@ -111,11 +81,10 @@ def doTheQuery(request , project_id):
except ValueError:
raise Http404()
# do we have a valid project?
project = (session
.query(Node)
.filter(Node.id == project_id)
.filter(Node.typename == 'PROJECT')
).first()
project = (session.query( Node )
.filter(Node.id == project_id)
.filter(Node.typename == 'PROJECT')
).first()
if project is None:
raise Http404()
......@@ -130,7 +99,7 @@ def doTheQuery(request , project_id):
if request.method == "POST":
queries = request.POST["query"]
name = request.POST["string"]
name = request.POST["string"]
# here we just realize queries already prepared by getGlobalStats
# ===> no need to repeat N parameter like in testISTEX <===
......@@ -147,7 +116,6 @@ def doTheQuery(request , project_id):
urlreqs.append( instancia.medlineEfetchRAW( yearquery ) )
alist = ["tudo fixe" , "tudo bem"]
resourcetype = RESOURCETYPES['name']['Pubmed (xml format)']
# corpus node instanciation as a Django model
corpus = Node(
......@@ -155,8 +123,9 @@ def doTheQuery(request , project_id):
user_id = request.user.id,
parent_id = project_id,
typename = 'CORPUS',
language_id = None,
hyperdata = {'Processing' : "Parsing documents",}
hyperdata = { "action" : "Scraping data"
, "language_id" : None
}
)
session.add(corpus)
session.commit()
......@@ -177,22 +146,21 @@ def doTheQuery(request , project_id):
t.daemon = True # thread dies when main thread (only non-daemon thread) exits.
t.start()
for url in urlreqs:
filename = MEDIA_ROOT + '/corpora/%s/%s' % (request.user, str(datetime.datetime.now().isoformat()))
tasks.q.put( [url , filename]) #put a task in th queue
tasks.q.put( url ) #put a task in the queue
tasks.q.join() # wait until everything is finished
dwnldsOK = 0
for filename in tasks.firstResults:
if filename!=False:
for filename in tasks.firstResults :
print(filename)
if filename != False:
# add the uploaded resource to the corpus
add_resource(corpus,
user_id = request.user.id,
type_id = resourcetype.id,
file = filename,
)
corpus.add_resource( type = 3
, path = filename
)
dwnldsOK+=1
if dwnldsOK == 0: return JsonHttpResponse(["fail"])
if dwnldsOK == 0 :
return JsonHttpResponse(["fail"])
try:
scheduled(parse_extract_indexhyperdata(corpus_id,))
......@@ -200,118 +168,10 @@ def doTheQuery(request , project_id):
print('WORKFLOW ERROR')
print(error)
sleep(1)
return HttpResponseRedirect('/project/' + str(project_id))
return HttpResponseRedirect('/projects/' + str(project_id))
data = alist
return JsonHttpResponse(data)
def testISTEX(request , project_id):
print("testISTEX:")
print(request.method)
alist = ["bar","foo"]
# implicit global session
# do we have a valid project id?
try:
project_id = int(project_id)
except ValueError:
raise Http404()
# do we have a valid project?
project = (session
.query(Node)
.filter(Node.id == project_id)
.filter(Node.typename == 'PROJECT')
).first()
if project is None:
raise Http404()
# do we have a valid user?
user = request.user
if not user.is_authenticated():
return redirect('/auth/?next=%s' % request.path)
if project.user_id != user.id:
return HttpResponseForbidden()
if request.method == "POST":
query = "-"
query_string = "-"
N = 0
if "query" in request.POST:
query = request.POST["query"]
query_string = query.replace(" ","+") # url encoded q
if "N" in request.POST:
N = int(request.POST["N"]) # query_size from views_opti
if N > QUERY_SIZE_N_MAX:
msg = "Invalid sample size N = %i (max = %i)" % (N, QUERY_SIZE_N_MAX)
print("ERROR (scrap: istex d/l ): ",msg)
raise ValueError(msg)
print("Scrapping Istex: '%s' (%i)" % (query_string , N))
urlreqs = []
pagesize = 50
tasks = MedlineFetcher()
chunks = list(tasks.chunks(range(N), pagesize))
for k in chunks:
if (k[0]+pagesize)>N: pagesize = N-k[0]
urlreqs.append("http://api.istex.fr/document/?q="+query_string+"&output=*&"+"from="+str(k[0])+"&size="+str(pagesize))
resourcetype = RESOURCETYPES["name"]["ISTex"]
# corpus node instanciation as a Django model
corpus = Node(
name = query,
user_id = request.user.id,
parent_id = project_id,
typename = 'CORPUS',
language_id = None,
hyperdata = {'Processing' : "Parsing documents",}
)
session.add(corpus)
session.commit()
corpus_id = corpus.id
print("NEW CORPUS", corpus_id)
ensure_dir(request.user)
tasks = MedlineFetcher()
for i in range(8):
t = threading.Thread(target=tasks.worker2) #thing to do
t.daemon = True # thread dies when main thread (only non-daemon thread) exits.
t.start()
for url in urlreqs:
filename = MEDIA_ROOT + '/corpora/%s/%s' % (request.user, str(datetime.datetime.now().isoformat()))
tasks.q.put( [url , filename]) #put a task in th queue
tasks.q.join() # wait until everything is finished
dwnldsOK = 0
for filename in tasks.firstResults:
if filename!=False:
# add the uploaded resource to the corpus
corpus.add_resource(corpus,
user_id = request.user.id,
type_id = resourcetype.id,
file = filename,
)
dwnldsOK+=1
if dwnldsOK == 0: return JsonHttpResponse(["fail"])
###########################
###########################
try:
scheduled(parse_extract_indexhyperdata(corpus_id,))
except Exception as error:
print('WORKFLOW ERROR')
print(error)
sleep(1)
return HttpResponseRedirect('/project/' + str(project_id))
data = [query_string,query,N]
return JsonHttpResponse(data)
scrapers/urls.py
View file @ 9eead9fa
......@@ -10,7 +10,11 @@ import scrapers.pubmed as pubmed
# Available databases : Pubmed, IsTex, (next: CERN)
# /!\ urls patterns here are *without* the trailing slash
urlpatterns = [ url(r'^pubmed/query$', pubmed.getGlobalStats)
urlpatterns = [ url(r'^pubmed/query$' , pubmed.getGlobalStats )
, url(r'^pubmed/search/(\d+)' , pubmed.doTheQuery )
# , url(r'^istex/query$' , pubmed.getGlobalStatsISTEXT )
# , url(r'^istex/search/(\d+)' , pubmed.testISTEX )
#, url(r'^scraping$' , scraping.Target.as_view() )
,
]
templates/pages/projects/project.html
View file @ 9eead9fa
......@@ -260,7 +260,7 @@
$.ajax({
// contentType: "application/json",
url: window.location.origin+"/tests/project/"+projectid+"/pubmedquery/go",
url: window.location.origin+"/scrapers/pubmed/search/"+projectid,
data: pubmedifiedQuery,
type: 'POST',
beforeSend: function(xhr) {
......
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