Merge branch 'testing' into stable

backupdb.py

+import os
+command = 'export PGPASSWORD=C8kdcUrAQy66U\npg_dump -U alexandre -h localhost gargandb| gzip > %s' % "mysqldump.db"
+os.system(command)

gargantext_web/urls.py

@@ -70,6 +70,7 @@ urlpatterns = patterns('',
     url(r'^tests/mvc$', views.tests_mvc),
     url(r'^tests/mvc-listdocuments$', views.tests_mvc_listdocuments),
 
+    url(r'^tests/istextquery$', pubmedscrapper.getGlobalStatsISTEXT),
     url(r'^tests/pubmedquery$', pubmedscrapper.getGlobalStats),
     url(r'^tests/project/(\d+)/pubmedquery/go$', pubmedscrapper.doTheQuery),
     url(r'^tests/project/(\d+)/ISTEXquery/go$', pubmedscrapper.testISTEX)

node/admin.py

@@ -125,8 +125,8 @@ class CustomForm(forms.Form):
         #     file_.name = str(datetime.now().microsecond)
         #     # raise forms.ValidationError(_('Come on dude, name too long. Now is:'+file_.name))
         # #File size
-        if len(file_)>104857600:
-            raise forms.ValidationError(_('File to heavy! (<100MB).'))
+        # if len(file_)>104857600:
+        #     raise forms.ValidationError(_('File to heavy! (<100MB).'))
         ## File type:
         # if file_.content_type == "application/zip":
         #     raise forms.ValidationError(_('We need a zip pls.'))

node/models.py

@@ -81,7 +81,6 @@ class NodeQuerySet(CTENodeManager.CTEQuerySet):
         metadata_cache = {metadata.name: metadata for metadata in Metadata.objects.all()}
         data = []
         for node in self:
-            print(node.id)
             for key, value in node.metadata.items():
                 if key in metadata_cache:
                     metadata = metadata_cache[key]
@@ -249,13 +248,14 @@ class Node(CTENode):
     @current_app.task(filter=task_method)
     def workflow(self, keys=None, ngramsextractorscache=None, ngramscaches=None, verbose=False):
         import time
-
+        total = 0
         print("LOG::TIME: In workflow()    parse_resources()")
         start = time.time()
         self.metadata['Processing'] = 1
         self.save()
         self.parse_resources()
         end = time.time()
+        total += (end - start)
         print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" parse_resources() [s]",(end - start))
         print("LOG::TIME: In workflow()    / parse_resources()")
 
@@ -266,7 +266,7 @@ class Node(CTENode):
         self.children.filter(type_id=type_document.pk).extract_ngrams(keys=['title',])
         end = time.time()
         print("- - - - - - - - - - \n")
-        print ("LOG::TIME: ",(end - start))
+        total += (end - start)
         print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" extract_ngrams() [s]",(end - start))
         print("LOG::TIME: In workflow()    / extract_ngrams()")
         
@@ -275,9 +275,9 @@ class Node(CTENode):
         from analysis.functions import do_tfidf
         do_tfidf(self)
         end = time.time()
+        total += (end - start)
         print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" do_tfidf() [s]",(end - start))
         print("LOG::TIME: In workflow()    / do_tfidf()")
-
         print("In workflow() END")
         self.metadata['Processing'] = 0
         self.save()

parsing/FileParsers/PubmedFileParser.py

@@ -80,12 +80,19 @@ class PubmedFileParser(FileParser):
             if len(RealDate)>4:
                 if len(RealDate)>8:
                     try: Decision = datetime.strptime(RealDate, '%Y %b %d').date()
-                    except: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
+                    except: 
+                        try: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
+                        except: Decision=False
                 else: 
                     try: Decision = datetime.strptime(RealDate, '%Y %b').date()
-                    except: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
-            else: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
+                    except: 
+                        try: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
+                        except: Decision=False
+            else: 
+                try: Decision = datetime.strptime(PubmedDate, '%Y %m %d').date()
+                except: Decision=False
 
+            if Decision!=False:
                 if "publication_year" in metadata: metadata["publication_year"] = str(Decision.year)
                 if "publication_month" in metadata: metadata["publication_month"] = str(Decision.month)
                 if "publication_day" in metadata: metadata["publication_day"] = str(Decision.day)

scrap_pubmed/MedlineFetcherDavid2015.py

@@ -12,6 +12,7 @@ import time
 from lxml import etree
 import datetime
 from django.core.files import File
+import codecs
 
 import threading
 from queue import Queue
@@ -39,6 +40,7 @@ class MedlineFetcher:
 
         "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')
             
@@ -92,10 +94,10 @@ class MedlineFetcher:
     def downloadFile(self, item):
         url = item[0]
         filename = item[1]
-        print("\tin downloadFile:")
-        print(url,filename)
+        print("\tin test_downloadFile:")
+        # print(url,filename)
         data = urlopen(url)
-        f = open(filename, 'w')
+        f = codecs.open(filename, "w" ,encoding='utf-8')
         myfile = File(f)
         myfile.write( data.read().decode('utf-8') )
         myfile.close()
@@ -104,6 +106,13 @@ class MedlineFetcher:
             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):
@@ -123,7 +132,10 @@ class MedlineFetcher:
     def worker2(self):
         while True:
             item = self.q.get()
-            self.firstResults.append(self.downloadFile(item))
+            results = []
+            try: result = self.downloadFile(item)
+            except: result = False
+            self.firstResults.append(result)
             self.q.task_done()
 
     def chunks(self , l , n):

scrap_pubmed/views.py

@@ -43,6 +43,32 @@ def getGlobalStats(request ):
 	return JsonHttpResponse(data)
 
 
+
+def getGlobalStatsISTEXT(request ):
+	print(request.method)
+	alist = ["bar","foo"]
+
+	if request.method == "POST":
+		N = 100
+		query = request.POST["query"]
+		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
+
+		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):
 	alist = ["hola","mundo"]
 
@@ -85,10 +111,7 @@ def doTheQuery(request , project_id):
 
 		corpus.save()
 
-		try:
 		tasks = MedlineFetcher()
-			tasks.ensure_dir ( MEDIA_ROOT + '/corpora/'+str(request.user)+"/" ) 
-			# configuring your queue with the event
 		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.
@@ -97,8 +120,14 @@ def doTheQuery(request , project_id):
 			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:
 				corpus.add_resource( user=request.user, type=resource_type, file=filename )
+				dwnldsOK+=1
+			
+		if dwnldsOK == 0: return JsonHttpResponse(["fail"])
 
 		# do the WorkFlow
 		try:
@@ -113,9 +142,6 @@ def doTheQuery(request , project_id):
 
 		return JsonHttpResponse(["workflow","finished","outside the try-except"])
 
-		except Exception as error:
-			print("lele",error)
-
 	data = alist
 	return JsonHttpResponse(data)
 
@@ -146,7 +172,8 @@ def testISTEX(request , project_id):
 			urlreqs.append("http://api.istex.fr/document/?q="+query_string+"&output=*&"+"from="+str(k[0])+"&size="+str(pagesize))
 		print(urlreqs)
 
-		# urlreqs = ["http://localhost/374255" , "http://localhost/374278" ]
+		urlreqs = ["http://localhost/374255" , "http://localhost/374278" ]
+		print(urlreqs)
 
 		resource_type = ResourceType.objects.get(name="istext" )
 

templates/project.html

@@ -313,6 +313,9 @@
 			console.log("disabling "+"#"+value.id)
 			$("#"+value.id).prop('onclick',null);
 
+			var theType = $("#id_type option:selected").html();
+
+			if(theType=="pubmed") {
 			    $.ajax({
 				  // contentType: "application/json",
 			      url: window.location.origin+"/tests/pubmedquery",
@@ -348,9 +351,49 @@
 			    });	
 			}
 
+			if(theType=="istext") {
+				console.log(window.location.origin+"tests/istextquery")
+			    $.ajax({
+				  // contentType: "application/json",
+			      url: window.location.origin+"/tests/istextquery",
+			      data: formData,
+			      type: 'POST',
+			      beforeSend: function(xhr) {
+			        xhr.setRequestHeader("X-CSRFToken", getCookie("csrftoken"));
+			      },
+			      success: function(data) {
+					console.log("in getGlobalResults")
+			        console.log(data)
+					console.log("enabling "+"#"+value.id)
+					$("#"+value.id).attr('onclick','getGlobalResults(this);');
+					// $("#submit_thing").prop('disabled' , false)
+					$("#submit_thing").html("Process a 100 sample!")
+
+		            thequeries = data
+		            var N=data.length,k=0;
+		            console.log("N: "+N)
+		            // for(var i in thequeries) N += thequeries[i].count
+		            if( N>1) {
+		            	var total = JSON.parse(data).total
+		            	$("#theresults").html("<i> <b>"+pubmedquery+"</b>: "+total+" publications.</i><br>")
+		            	$('#submit_thing').prop('disabled', false);
+		            } else {
+		            	$("#theresults").html("<i>  <b>"+data[0]+"</b></i><br>")
+		            	$('#submit_thing').prop('disabled', true);
+		            }
+
+			      },
+			        error: function(result) {
+			            console.log("Data not found");
+			        }
+			    });	
+			}
+		}
+
 		// CSS events for selecting one Radio-Input
 		function FileOrNotFile( value ) {
 			var showfile = JSON.parse(value)
+			var theType = $("#id_type option:selected").html();
 			// @upload-file events
 			if (showfile) {
 				console.log("You've clicked the YES") 
@@ -376,7 +419,7 @@
 
 				$( "#id_name" ).on('input',function(e){
 					console.log($(this).val())
-					testAjax( $(this).val() )
+					if(theType=="pubmed") testPUBMED( $(this).val() )
 				}); 
 			}
 		}
@@ -384,8 +427,8 @@
 		//CSS events for changing the Select element
 		function CustomForSelect( selected ) {
 			// show Radio-Inputs and trigger FileOrNotFile>@upload-file events
-			if(selected=="pubmed") {
-				console.log("show the button")
+			if(selected=="pubmed" || selected=="istext") {
+				console.log("show the button for: "+selected)
 				$("#pubmedcrawl").css("visibility", "visible"); 
 				$("#pubmedcrawl").show();
 				$("#file_yes").click();
@@ -414,7 +457,7 @@
  			return data;
  		}
 
-		function testAjax( query ) {
+		function testPUBMED( query ) {
 			LastData = []
 			if(!query || query=="") return;
 			var pubmedquery = encodeURIComponent(query)
@@ -450,7 +493,7 @@
 		      success: function(data) {
 				console.log("ajax_success: in testISTEX()")
 		        console.log(data)
-		        location.reload();
+		        // location.reload();
 		      },
 		        error: function(result) {
 		            console.log("in testISTEX(). Data not found");