diff --git a/interactive-mining-madoap/madoap/src/madserverv2.py b/interactive-mining-madoap/madoap/src/madserverv2.py
index 64a4a17..042864b 100755
--- a/interactive-mining-madoap/madoap/src/madserverv2.py
+++ b/interactive-mining-madoap/madoap/src/madserverv2.py
@@ -113,6 +113,16 @@ def numberOfDocsUploaded(user_id):
             return num_lines
     return 0
 
+def deleteAllUserFiles(user_id):
+    if user_id:
+        file_name = "/tmp/p%s.tsv" % (user_id)
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+        file_name = "/tmp/docs%s.json" % (user_id)
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+
+
 class BaseHandler(ozhandler.DjangoErrorMixin, ozhandler.BasicAuthMixin, tornado.web.RequestHandler):
     def __init__(self, *args):
         tornado.web.RequestHandler.__init__(self, *args)
@@ -299,9 +309,6 @@ class createUploadProfileHandler(BaseHandler):
     def get(self):
         if 'data' in self.request.arguments:
             return
-        elif 'reset' in self.request.arguments:
-            # TODO RESET everything
-            print "TODO RESET everything"
         else:
             # check if we already gave client a user_id
             user_id = self.get_secure_cookie('madgikmining')
@@ -373,19 +380,23 @@ class uploadCodesHandler(BaseHandler):
     def get(self):
         if 'data' in self.request.arguments:
             return
-        else:
-            # check if we already gave client a user_id
-            user_id = self.get_secure_cookie('madgikmining')
-            if user_id is None:
-                return 
-            # check if he already uploaded his grants ids and inform him via a message
-            self.render('upload_codes.html', settings=msettings)
+        # check if we gave client a user_id
+        user_id = self.get_secure_cookie('madgikmining')
+        if user_id is None:
+            return 
+        if 'new' in self.request.arguments and self.request.arguments['new'][0] == '1':
+            msettings.RESET_FIELDS = 1
+            # reset everything
+            deleteAllUserFiles(user_id)
+        # check if he already uploaded his grants ids and inform him via a message
+        self.render('upload_codes.html', settings=msettings)
     def post(self):
         try:
             # get user id from cookie. Must have
             user_id = self.get_secure_cookie('madgikmining')
             if user_id is None:
                 return
+            # service to upload a tsv file with the codes. Returns the codes
             if 'upload' in self.request.files:
                 # get file info and body from post data
                 fileinfo = self.request.files['upload'][0]
@@ -398,7 +409,7 @@ class uploadCodesHandler(BaseHandler):
                 codes = {}
                 lines = fileinfo['body'].splitlines()
                 for line in lines:
-                    columns = re.split(r'\t+', line.rstrip('\t'))
+                    columns = re.split(r'\t+', line.rstrip('\t\n\r'))
                     if len(columns) and columns[0] == '':
                         continue
                     elif len(columns) > 1:
@@ -415,12 +426,15 @@ class uploadCodesHandler(BaseHandler):
                     self.set_secure_cookie('madgikmining_grantsuploaded', str(len(lines)))
                 self.write(json.dumps(data))
                 self.finish()
+            # service to store the final user codes. Returns the number of the codes
             elif 'concepts' in self.request.arguments and self.request.arguments['concepts'][0] != '{}':
                 # write data to physical file
                 cname = "/tmp/p{0}.tsv".format(user_id)
                 fh = open(cname, 'w')
                 concepts = json.loads(self.request.arguments['concepts'][0])
                 for key, value in concepts.iteritems():
+                    if key == '':
+                        continue
                     fh.write("{0}\t{1}\n".format(key,value))
                 fh.close()
                 # data to be sent
@@ -432,6 +446,28 @@ class uploadCodesHandler(BaseHandler):
                     self.set_secure_cookie('madgikmining_grantsuploaded', str(len(concepts)))
                 self.write(json.dumps(data))
                 self.finish()
+            # service to return the already uploaded user codes
+            elif 'already' in self.request.arguments:
+                data = {}
+                data['data'] = {}
+                file_name = "/tmp/p%s.tsv" % (user_id)
+                if os.path.isfile(file_name):
+                    codes = {}
+                    num_lines = 0
+                    for line in open(file_name):
+                        columns = re.split(r'\t+', line.rstrip('\t\n\r'))
+                        if len(columns) and columns[0] == '':
+                            continue
+                        elif len(columns) > 1:
+                            codes[columns[0]] = columns[1]
+                        elif len(columns) == 1:
+                            codes[columns[0]] = ''
+                        num_lines += 1
+                    cookie = self.get_secure_cookie('madgikmining_grantsuploaded')
+                    if cookie and str(num_lines) == cookie:
+                        data['data'] = codes
+                self.write(json.dumps(data))
+                self.finish()
 
         except Exception as ints:
             data = {}
@@ -452,9 +488,12 @@ class configureProfileHandler(BaseHandler):
             # check if we already gave client a user_id
             user_id = self.get_secure_cookie('madgikmining')
             if user_id is None:
-                return 
-            # check if he already uploaded his grants ids and inform him via a message
-            self.render('configure_profile.html', settings=msettings)
+                return
+            # check if he uploaded his codes
+            if numberOfGrantsUploaded(user_id, self.get_secure_cookie('madgikmining_grantsuploaded')):
+                self.render('configure_profile.html', settings=msettings)
+            else:
+                self.redirect('/upload-codes')
     def post(self):
         try:
             # get user id from cookie. Must have
@@ -508,15 +547,17 @@ class configureProfileHandler(BaseHandler):
                         os.remove(cname)
                         print e
                         return
-                data['respond'] = "<b>File {0}</b> uploaded successfully!".format(fname)
+                file_name = "/tmp/docs%s.json" % (user_id)
+                if os.path.isfile(file_name):
+                    data['data'] = sum(1 for line in open(file_name))
                 self.write(json.dumps(data))
                 self.finish()
             # post case where the user selects form preset documents samples
             elif 'doc_sample' in self.request.arguments and self.request.arguments['doc_sample'][0] != '':
 
                 sample_file_name = ""
-                if self.request.arguments['doc_sample'][0] == "nih_sample":
-                    sample_file_name = "static/nih_sample.tsv"
+                if self.request.arguments['doc_sample'][0] == "egi_sample":
+                    sample_file_name = "static/egi_sample.tsv"
                 elif self.request.arguments['doc_sample'][0] == "rcuk_sample":
                     sample_file_name = "static/rcuk_sample.tsv"
                 elif self.request.arguments['doc_sample'][0] == "arxiv_sample":
@@ -524,7 +565,7 @@ class configureProfileHandler(BaseHandler):
                 sample_file = open(sample_file_name, 'r')
 
                 # write data to physical file
-                cname = "/tmp/docs{0}/json".format(user_id)
+                cname = "/tmp/docs{0}.json".format(user_id)
                 fh = open(cname, 'w')
                 while 1:
                     copy_buffer = sample_file.read(1048576)
@@ -532,14 +573,27 @@ class configureProfileHandler(BaseHandler):
                         break
                     fh.write(copy_buffer)
                 fh.close()
+                lines_num = sum(1 for line in open(cname))
                 
                 # data to be sent
                 data = {}
-                if len(concepts) == 0:
+                if lines_num == 0:
                     data['error'] = "You have to provide at least one concept to continue"
                 else:
-                    data['respond'] = "<b>{0} Codes</b> loaded successfully!".format(len(concepts))
-                    self.set_secure_cookie('madgikmining_grantsuploaded', str(len(concepts)))
+                    data['data'] = lines_num
+                self.write(json.dumps(data))
+                self.finish()
+            # service to return the already uploaded documents
+            elif 'already' in self.request.arguments:
+                data = {}
+                if msettings.RESET_FIELDS == 1:
+                    data['data'] = -1
+                else:
+                    data['data'] = 0
+                file_name = "/tmp/docs%s.json" % (user_id)
+                if os.path.isfile(file_name):
+                    data['data'] = sum(1 for line in open(file_name))
+                msettings.RESET_FIELDS = 0
                 self.write(json.dumps(data))
                 self.finish()
             # post case for the actual mining proccess
@@ -549,16 +603,20 @@ class configureProfileHandler(BaseHandler):
                 # create positive and negative words weighted regex text
                 pos_set = neg_set = conf = whr_conf = ''
                 if 'poswords' in self.request.arguments and self.request.arguments['poswords'][0] != '{}':
+                    data['poswords'] = []
                     # construct math string for positive words matching calculation with weights
                     pos_words = json.loads(self.request.arguments['poswords'][0])
                     for key, value in pos_words.iteritems():
                         pos_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s + ' % (key,value)
+                        data['poswords'].append(key)
                     pos_set += "0"
                 if 'negwords' in self.request.arguments and self.request.arguments['negwords'][0] != '{}':
+                    data['negwords'] = []
                     # construct math string for negative words matching calculation with weights
                     neg_words = json.loads(self.request.arguments['negwords'][0])
                     for key, value in neg_words.iteritems():
                         neg_set += r'regexpcountuniquematches("(?:\b)%s(?:\b)",j2s(prev,middle,next))*%s - ' % (key,value)
+                        data['negwords'].append(key)
                     neg_set += "0"
                 if pos_set != '' and neg_set != '':
                     conf = ", ({0} - {1})".format(pos_set, neg_set)
@@ -574,8 +632,8 @@ class configureProfileHandler(BaseHandler):
                 cursor=msettings.Connection.cursor()
 
                 if numberOfDocsUploaded(user_id) != 0:
-                    doc_filters = "regexpr('[\n|\r]',c2,' ')"
-                    ackn_filters = "regexpr(\"\\'\", c2,'')"
+                    doc_filters = "regexpr('[\n|\r]',d2,' ')"
+                    ackn_filters = "regexpr(\"\\'\", p2,'')"
                     if 'punctuation' in self.request.arguments and self.request.arguments['punctuation'][0] == "1":
                         doc_filters = 'keywords('+doc_filters+')'
                         ackn_filters = 'keywords('+ackn_filters+')'
@@ -590,10 +648,10 @@ class configureProfileHandler(BaseHandler):
                         doc_filters = 'filterstopwords('+doc_filters+')'
                         ackn_filters = 'filterstopwords('+ackn_filters+')'
                     list(cursor.execute("drop table if exists grantstemp"+user_id, parse=False))
-                    query_pre_grants = "create temp table grantstemp{0} as select stripchars(c1) as c1, case when c2 is null then null else {1} end as c2 from (setschema 'c1,c2' file '/tmp/p{0}.tsv' dialect:tsv)".format(user_id, ackn_filters)
+                    query_pre_grants = "create temp table grantstemp{0} as select stripchars(p1) as gt1, case when p2 is null then null else {1} end as gt2 from (setschema 'p1,p2' file '/tmp/p{0}.tsv' dialect:tsv)".format(user_id, ackn_filters)
                     cursor.execute(query_pre_grants)
                     list(cursor.execute("drop table if exists docs"+user_id, parse=False))
-                    query1 = "create temp table docs{0} as select c1, {1} as c2 from (setschema 'c1,c2' select jsonpath(c1, '$.id', '$.text') from (file '/tmp/docs{0}.json'))".format(user_id, doc_filters)
+                    query1 = "create temp table docs{0} as select d1, {1} as d2 from (setschema 'd1,d2' select jsonpath(c1, '$.id', '$.text') from (file '/tmp/docs{0}.json'))".format(user_id, doc_filters)
                     cursor.execute(query1)
                 else:
                     data['error'] = "You have to provide at least one concept to continue"
@@ -606,23 +664,33 @@ class configureProfileHandler(BaseHandler):
                 if 'wordssplitnum' in self.request.arguments and self.request.arguments['wordssplitnum'][0] != '':
                     words_split = int(self.request.arguments['wordssplitnum'][0])
                     if 0 < words_split and words_split <= 10:
-                        acknowledgment_split = r'textwindow2s(regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", c2, "\\\1"),0,'+str(words_split)+r',0)'
+                        acknowledgment_split = r'textwindow2s(regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", gt2, "\\\1"),0,'+str(words_split)+r',0)'
                     else:
-                        acknowledgment_split = r'"prev" as prev, regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", c2, "\\\1") as middle, "next" as next'
-                    query0 = r"create temp table grants"+user_id+r' as select c1 as c3, jmergeregexp(jgroup("(?<=[\s\b])"||middle||"(?=[\s\b])")) as c4 from '+r"(setschema 'c1,prev,middle,next' select c1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (c1 or c1!="") and c2 not null) group by c1 union all select distinct c1 as c3, "(?!.*)" as c4 from grantstemp'+user_id+r" where (c1 or c1!='') and c2 is null"
+                        acknowledgment_split = r'"prev" as prev, regexpr("([\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|])", gt2, "\\\1") as middle, "next" as next'
+                    # query0 = r"create temp table grants"+user_id+r' as select gt1 as g1, jmergeregexp(jgroup("(?<=[\s\b])"||middle||"(?=[\s\b])")) as g2 from '+r"(setschema 'gt1,prev,middle,next' select gt1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (gt1 or gt1!="") and gt2 not null) group by gt1 union all select distinct gt1 as g1, "(?!.*)" as g2 from grantstemp'+user_id+r" where (gt1 or gt1!='') and gt2 is null"
+                    query0 = r"create temp table grants"+user_id+r' as select gt1 as g1, jmergeregexp(jgroup(middle)) as g2 from '+r"(setschema 'gt1,prev,middle,next' select gt1, "+acknowledgment_split+r' from grantstemp'+user_id+r' where (gt1 or gt1!="") and gt2 not null) group by gt1 union all select distinct gt1 as g1, "(?!.*)" as g2 from grantstemp'+user_id+r" where (gt1 or gt1!='') and gt2 is null"
                     cursor.execute(query0)
+                    query0get = "select * from grants{0}".format(user_id)
+                    results0get = [r for r in cursor.execute(query0get)]
+                    print results0get
 
-                query2 = "select c1, c3, max(confidence) as confidence from (select c1, c3, regexpcountuniquematches(c4, j2s(prev,middle,next)) as confidence {0} from (select c1, textwindow2s(c2,10,1,5) from (select * from docs{1})), (select c3, c4 from grants{1}) T where middle = T.c3 {2}) group by c1".format(conf, user_id, whr_conf)
+                query2 = "select d1, g1, context, acknmatch, max(confidence) as confidence from (select d1, g1, regexpcountuniquematches(g2, j2s(prev,middle,next)) as confidence, j2s(prev,middle,next) as context, regexprfindall(g2, j2s(prev,middle,next)) as acknmatch {0} from (select d1, textwindow2s(d2,20,1,20) from (select * from docs{1})), (select g1, g2 from grants{1}) T where middle = T.g1 {2}) group by d1".format(conf, user_id, whr_conf)
                 # query2 = "select c1, c3 {0} from (select c1, textwindow2s(c2,10,1,5) from (select * from docs{1})), (select c3 from grants{1}) T where middle = T.c3 {2}".format(conf, user_id, whr_conf)
                 results = [r for r in cursor.execute(query2)]
-                data['funding_info'] = [{"code": r[1]} for r in results]
+                print results
+                doctitles = {}
+                for r in results:
+                    if r[0] not in doctitles:
+                        doctitles[r[0]] = []
+                    doctitles[r[0]].append({"match": r[1], "context": r[2], "acknmatch": json.loads(r[3]), "confidence": r[4]})
+                data['matches'] = doctitles
                 self.write(json.dumps(data))
                 self.flush()
                 self.finish()
 
         except Exception as ints:
             data = {}
-            data['error'] = "<b style=\"color: red\">File Failed to Upload!</b>"
+            data['error'] = "<b style=\"color: red\">Something went very very wrong!</b>"
             self.write(json.dumps(data))
             self.finish()
             print ints
@@ -639,13 +707,104 @@ class saveProfileHandler(BaseHandler):
     def get(self):
         if 'data' in self.request.arguments:
             return
+        elif 'saveprofile' in self.request.arguments and self.request.arguments['saveprofile'][0] == '1':
+            user_id = self.get_secure_cookie('madgikmining')
+            if user_id is None:
+                return
+            profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
+            buf_size = 4096
+            self.set_header('Content-Type', 'application/octet-stream')
+            self.set_header('Content-Disposition', 'attachment; filename=' + "OAMiningProfile_{0}.oamp".format(user_id))
+            self.flush()
+            with open(profile_file_name, 'r') as f:
+                while True:
+                    data = f.read(buf_size)
+                    if not data:
+                        break
+                    self.write(data)
+            self.finish()
         else:
             # check if we already gave client a user_id
             user_id = self.get_secure_cookie('madgikmining')
             if user_id is None:
-                return 
-            # check if he already uploaded his grants ids and inform him via a message
-            self.render('save_profile.html', settings=msettings)
+                return
+            # check if he uploaded his codes
+            if numberOfGrantsUploaded(user_id, self.get_secure_cookie('madgikmining_grantsuploaded')):
+                self.render('save_profile.html', settings=msettings)
+            else:
+                self.redirect('/upload-codes')
+    def post(self):
+        try:
+            # get user id from cookie. Must have
+            user_id = self.get_secure_cookie('madgikmining')
+            if user_id is None:
+                return
+            # post case where the profile data is uploaded to create the profile file
+            if 'createprofile' in self.request.arguments and self.request.arguments['createprofile'][0] == '1':
+                import sys
+                sys.path.append(msettings.MADIS_PATH)
+                import madis
+                # get the database cursor
+                # profile file name
+                profile_file_name = "/tmp/OAMiningProfile_{0}.oamp".format(user_id)
+                cursor=madis.functions.Connection(profile_file_name).cursor()
+                # Create poswords table
+                cursor.execute("drop table if exists poswords", parse=False)
+                cursor.execute("create table poswords(c1,c2)", parse=False)
+                # Create negwords table
+                cursor.execute("drop table if exists negwords", parse=False)
+                cursor.execute("create table negwords(c1,c2)", parse=False)
+                # Create filters table
+                cursor.execute("drop table if exists filters", parse=False)
+                cursor.execute("create table filters(c1,c2)", parse=False)
+                # Create grants table
+                cursor.execute("drop table if exists grants", parse=False)
+                cursor.execute("create table grants(c1)", parse=False)
+                if 'poswords' in self.request.arguments and self.request.arguments['poswords'][0] != '{}':
+                    # construct math string for positive words matching calculation with weights
+                    pos_words = json.loads(self.request.arguments['poswords'][0])
+                    cursor.executemany("insert into poswords(c1,c2) values(?,?)",
+                              (
+                                    (key, value,) for key, value in pos_words.iteritems()
+                              )
+                    )
+                if 'negwords' in self.request.arguments and self.request.arguments['negwords'][0] != '{}':
+                    # construct math string for negative words matching calculation with weights
+                    neg_words = json.loads(self.request.arguments['negwords'][0])
+                    cursor.executemany("insert into negwords(c1,c2) values(?,?)",
+                              (
+                                    (key, value,) for key, value in neg_words.iteritems()
+                              )
+                    )
+                if 'filters' in self.request.arguments and self.request.arguments['filters'][0] != '{}':
+                    # construct math string for negative words matching calculation with weights
+                    filters = json.loads(self.request.arguments['filters'][0])
+                    cursor.executemany("insert into filters(c1,c2) values(?,?)",
+                              (
+                                    (key, value,) for key, value in filters.iteritems()
+                              )
+                    )
+                if numberOfGrantsUploaded(user_id, self.get_secure_cookie('madgikmining_grantsuploaded')) != 0:
+                      cursor.execute("insert into grants select stripchars(c1) as c1 from (file '/tmp/p{0}.csv')".format(user_id))
+                cursor.close()
+
+                data = {}
+                data['data'] = 1
+                self.write(json.dumps(data))
+                self.flush()
+                self.finish()
+
+        except Exception as ints:
+            data = {}
+            data['error'] = "<b style=\"color: red\">Something went very very wrong!</b>"
+            self.write(json.dumps(data))
+            self.finish()
+            print ints
+
+        try:
+            cursor.close()
+        except:
+            pass
 
 
 class profileCreationHandler(BaseHandler):
diff --git a/interactive-mining-madoap/madoap/src/settings.py b/interactive-mining-madoap/madoap/src/settings.py
index 3b01a88..bddd8c0 100644
--- a/interactive-mining-madoap/madoap/src/settings.py
+++ b/interactive-mining-madoap/madoap/src/settings.py
@@ -9,6 +9,7 @@ WEB_SERVER_PORT=8080
 APPDIRNAME='openaireplus'
 MADIS_PATH='../../../interactive-mining-3rdparty-madis/madis/src'
 DB='static/database.db'
+RESET_FIELDS=1
 
 FLOW_PATH=''
 
diff --git a/interactive-mining-madoap/madoap/src/static/animations.css b/interactive-mining-madoap/madoap/src/static/animations.css
new file mode 100644
index 0000000..904d84c
--- /dev/null
+++ b/interactive-mining-madoap/madoap/src/static/animations.css
@@ -0,0 +1,102 @@
+/*ANIMATIONS*/
+tr.new-item {
+  opacity:0;
+  -webkit-animation:fadeIn .1s linear forwards;
+  -o-animation:fadeIn .1s linear forwards;
+  animation:fadeIn .1s linear forwards
+}
+@keyframes fadeIn {
+  to {
+    opacity:1
+  }
+}
+
+@keyframes openspace {
+  to {
+    height: auto
+  }
+}
+
+tr.removed-item {
+  -webkit-animation: removed-item-animation .3s cubic-bezier(.55,-0.04,.91,.94) forwards;
+  -o-animation: removed-item-animation .3s cubic-bezier(.55,-0.04,.91,.94) forwards;
+  animation: removed-item-animation .3s cubic-bezier(.55,-0.04,.91,.94) forwards
+}
+
+@keyframes removed-item-animation {
+  from {
+    opacity: 1;
+  }
+
+  to {
+    opacity: 0
+  }
+}
+
+@-webkit-keyframes new-item-animation {
+  from {
+    opacity: 0;
+    -webkit-transform: scale(0);
+    transform: scale(0)
+  }
+
+  to {
+    opacity: 1;
+    -webkit-transform: scale(1);
+    transform: scale(1)
+  }
+}
+
+@-o-keyframes new-item-animation {
+  from {
+    opacity: 0;
+    -o-transform: scale(0);
+    transform: scale(0)
+  }
+
+  to {
+    opacity: 1;
+    -o-transform: scale(1);
+    transform: scale(1)
+  }
+}
+
+@-webkit-keyframes openspace {
+  to {
+    height: auto
+  }
+}
+
+@-o-keyframes openspace {
+  to {
+    height: auto
+  }
+}
+
+@-webkit-keyframes removed-item-animation {
+  from {
+    opacity: 1;
+    -webkit-transform: scale(1);
+    transform: scale(1)
+  }
+
+  to {
+    -webkit-transform: scale(0);
+    transform: scale(0);
+    opacity: 0
+  }
+}
+
+@-o-keyframes removed-item-animation {
+  from {
+    opacity: 1;
+    -o-transform: scale(1);
+    transform: scale(1)
+  }
+
+  to {
+    -o-transform: scale(0);
+    transform: scale(0);
+    opacity: 0
+  }
+}
\ No newline at end of file
diff --git a/interactive-mining-madoap/madoap/src/static/configure-profile.js b/interactive-mining-madoap/madoap/src/static/configure-profile.js
index dde4994..b284800 100644
--- a/interactive-mining-madoap/madoap/src/static/configure-profile.js
+++ b/interactive-mining-madoap/madoap/src/static/configure-profile.js
@@ -34,67 +34,107 @@
         .on( 'blur', function(){ $input.removeClass( 'has-focus' ); });
     });
 
-    var match_level_choice = 0;
+    var match_level_choice = -1;
     var advanced_options_open = 0;
 
     var handleMatchLevelChoice = function() {
         $('#1-level').on('click', function( e ) {
             if (advanced_options_open) {
-                UIkit.accordion($('.uk-accordion')).toggle(0, true);
+                UIkit.accordion($('#advanced-opts-toggle')).toggle(0, true);
                 advanced_options_open = 0;
             }
             if (match_level_choice != 0) {
+                deleteAllWords(0,1);
+                deleteAllWords(0,0);
                 console.log('#1-level');
+                // store change to localstorage
+                localStorage.setItem('matchlevel', "#1-level");
+                // Add the positive words
+                addDataToTable(generateId(1), 'European Grid Infrastructure', 1, 1);
+                addDataToTable(generateId(1), 'EGI', 1, 1);
+                addDataToTable(generateId(1), 'European Grid Initiative', 1, 1);
             }
             match_level_choice = 0;
         });
         $('#2-level').on('click', function( e ) {
             if (advanced_options_open) {
-                UIkit.accordion($('.uk-accordion')).toggle(0, true);
+                UIkit.accordion($('#advanced-opts-toggle')).toggle(0, true);
                 advanced_options_open = 0;
             }
             if (match_level_choice != 1) {
+                deleteAllWords(0,1);
+                deleteAllWords(0,0);
                 console.log('#2-level');
+                // store change to localstorage
+                localStorage.setItem('matchlevel', "#2-level");
             }
             match_level_choice = 1;
         });
         $('#3-level').on('click', function( e ) {
             if (advanced_options_open) {
-                UIkit.accordion($('.uk-accordion')).toggle(0, true);
+                UIkit.accordion($('#advanced-opts-toggle')).toggle(0, true);
                 advanced_options_open = 0;
             }
             if (match_level_choice != 2) {
+                deleteAllWords(0,1);
+                deleteAllWords(0,0);
                 console.log('#3-level');
+                // store change to localstorage
+                localStorage.setItem('matchlevel', "#3-level");
             }
             match_level_choice = 2;
         });
         $('#c-level').on('click', function( e ) {
             if (advanced_options_open == 0) {
-                UIkit.accordion($('.uk-accordion')).toggle(0, true);
+                UIkit.accordion($('#advanced-opts-toggle')).toggle(0, true);
                 advanced_options_open = 1;
             }
             if (match_level_choice != 3) {
                 console.log('#c-level');
+                // store change to localstorage
+                localStorage.setItem('matchlevel', "#c-level");
             }
         });
-        $('.uk-accordion').on('show', function () {
+        // $('#advanced-opts-toggle').on('show', function () {
+        //     console.log('#GG-level');
+        //     UIkit.switcher($('#uk-switcher')).show(3);
+        //     UIkit.switcher($('.uk-switcher')).show(3);
+        //     advanced_options_open = 1;
+        // });
+        // $('#advanced-opts-toggle').on('hide', function () {
+        //     console.log('#BB-level');
+        //     UIkit.switcher($('#uk-switcher')).show(match_level_choice);
+        //     UIkit.switcher($('.uk-switcher')).show(match_level_choice);
+        //     advanced_options_open = 0;
+        // });
+        
+        $('#advanced-opts-toggle').on('show', function () {
             console.log('#GG-level');
-            UIkit.switcher($('#uk-switcher')).show(3);
-            UIkit.switcher($('.uk-switcher')).show(3);
             advanced_options_open = 1;
+            $('#c-level').click();
         });
-        $('.uk-accordion').on('hide', function () {
+        $('#advanced-opts-toggle').on('hide', function () {
             console.log('#BB-level');
-            UIkit.switcher($('#uk-switcher')).show(match_level_choice);
-            UIkit.switcher($('.uk-switcher')).show(match_level_choice);
             advanced_options_open = 0;
+            if (match_level_choice == 0) {
+                match_level_choice = 3;
+                $('#1-level').click();
+            } else if (match_level_choice == 1) {
+                match_level_choice = 3;
+                $('#2-level').click();
+            } else if (match_level_choice == 2) {
+                match_level_choice = 3;
+                $('#3-level').click();
+            }
         });
 
-        // UIkit.accordion($('.uk-accordion')).toggle(0, true);
+        // UIkit.accordion($('#advanced-opts-toggle')).toggle(0, true);
         // UIkit.switcher($('#uk-switcher')).show(3);
         // UIkit.switcher($('.uk-switcher')).show(3);
     }
 
+/////////// LIST FUNCTIONS
+
     var count_pos = 0, count_neg = 0;
 
     var updateCounter = function(is_pos){
@@ -128,31 +168,6 @@
         }
     }
 
-    var handleNextButton = function() {
-        $('#next-button').on('click', function( e ) {
-            console.log(JSON.stringify(wordsDataToArray()));
-            var formData = new FormData();
-            formData.append("concepts", JSON.stringify(wordsDataToArray()));
-            $.ajax({
-                url: "upload-codes",
-                type: 'POST',
-                data: formData,
-                async: false,
-                success: function (data) {
-                    console.log(JSON.parse(data).respond)
-                    window.location="configure-profile"
-                },
-                error: function (xhr, ajaxOptions, thrownError) {
-                  $('#file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
-                  // $('#file-uploaded')[0].checked = false;
-                },
-                cache: false,
-                contentType: false,
-                processData: false
-            });
-        });
-    }
-
     var wordsDataToArray = function(is_pos) {
         // TODO
         var data = {};
@@ -193,7 +208,7 @@
         if (isPhrase) {
             $(currentEle).html('<input class="uk-textarea thVal" style="word-break: break-word; width:100%" type="text" value="' + value + '" />');
         } else {
-            $(currentEle).html('<input style="width:100%" class="thVal" type="text" value="' + value + '" />');
+            $(currentEle).html('<input style="width:100%" class="thVal" type="number" min="0" max="100" value="' + value + '" />');
         }
         $(".thVal").focus();
         $(".thVal").keyup(function (event) {
@@ -202,7 +217,7 @@
                 var new_val = $(".thVal").val();
                 $(currentEle).html($(".thVal").val().trim());
                 if (isPhrase || (new_val != '' && !isNaN(new_val) && new_val >= 0 && new_val <= 100)) {
-                    $(currentEle).html($(".thVal").val().trim());
+                    $(currentEle).html($(".thVal").val());
                 } else {
                     $(currentEle).html(1);
                 }
@@ -241,16 +256,18 @@
 
     var removeWord = function(id, is_pos){
         var item = $('#' + id );
-
         item.addClass('removed-item')
           .one('webkitAnimationEnd oanimationend msAnimationEnd animationend', function(e) {
               $(this).remove();
         });
+        // remove from localstorage
+        localStorage.remove('#' + id);
         if (is_pos === 1) {
             count_pos--;
         } else {
             count_neg--;
         }
+        updateCounter(is_pos);
     };
 
     var count_pos = 0, count_neg = 0;
@@ -283,8 +300,8 @@
                                              }
                                           }
                       })));
-            addDoubleClick($(createdItem).find("div.phrase"));
-            addDoubleClick($(createdItem).find("div.weight"));
+            addDoubleClick($(createdItem).find("td.phrase"));
+            addDoubleClick($(createdItem).find("td.weight"));
             createdItem.on('keydown', function(ev){
                 if(ev.keyCode === 13) return false;
             });
@@ -295,6 +312,17 @@
               count_neg++;
               updateCounter(0);
             }
+            // store into localstorage
+            var obj = {};
+            obj["phrase"] = content_word;
+            obj["weight"] = content_weight;
+            localStorage.setItem(id, JSON.stringify(obj));
+            for(var key in localStorage){
+              if (key === null)
+                continue;
+              var json_string = localStorage.getItem(key);
+                console.log(key+' '+json_string);
+            }
         }
     }
 
@@ -325,7 +353,71 @@
                 input_weight.val('1');
             }
         });
-     };
+        updateCounter(1);
+        updateCounter(0);
+        handleDeleteButtons();
+    };
+
+    var deleteAllWords = function(warnUser = 1, is_pos) {
+        if(!warnUser || confirm('Are you sure you want to delete all the items in the list? There is no turning back after that.')){                 //remove items from DOM
+            if (is_pos) {
+                var items = $('tr[id ^= positive]');
+                items.addClass('removed-item').one('webkitAnimationEnd oanimationend msAnimationEnd animationend', function(e) {
+                  $(this).remove();
+                });
+                // Delete all pos from local storage
+                for(var key in localStorage){
+                    if (key === null)
+                        continue;
+                    var json_string = localStorage.getItem(key);
+                    if(key.indexOf('positive') === 0){
+                        localStorage.removeItem(key);
+                    }
+                }
+                count_pos = 0;
+                updateCounter(1);
+            } else {
+                var items = $('tr[id ^= negative]');
+                items.addClass('removed-item').one('webkitAnimationEnd oanimationend msAnimationEnd animationend', function(e) {
+                  $(this).remove();
+                });
+                // Delete all neg from local storage
+                for(var key in localStorage){
+                    if (key === null)
+                        continue;
+                    var json_string = localStorage.getItem(key);
+                    if(key.indexOf('negative') === 0){
+                        localStorage.removeItem(key);
+                    }
+                }
+                count_neg = 0;
+                updateCounter(0);
+            }
+        }
+    };
+
+    //handler for the "delete all" button
+    var handleDeleteButtons = function(){
+        $('#clear-all-pos').on('click', function() { deleteAllWords(1,1);});
+        $('#clear-all-neg').on('click', function() { deleteAllWords(1,0)});
+    };
+
+    var handleFiltersInput = function() {
+        $("#letter-case-select").on('change', function(e) {
+            localStorage.setItem('lettercase', $("#letter-case-select option:selected").text());
+        });
+        $("#word-split").on('change', function(e) {
+            localStorage.setItem('wordssplitnum', $("#word-split").val());
+        });
+        $("#stop-words-filter").on('change', function(e) {
+            localStorage.setItem('stopwords', $('#stop-words-filter').prop('checked')===true?1:0);
+            console.log('stop-words-filter '+localStorage.getItem('stopwords'));
+        });
+        $("#punctuation-filter").on('change', function(e) {
+            localStorage.setItem('punctuation', $('#punctuation-filter').prop('checked')===true?1:0);
+            console.log('punctuation-filter '+localStorage.getItem('punctuation'));
+        });
+    }
 
     var handleRunMiningButton = function() {
         $("#run-mining-btn").on('click', function( e ) {
@@ -348,7 +440,113 @@
                 data: formData,
                 async: false,
                 success: function (data) {
-                    console.log(data)
+                    obj = JSON && JSON.parse(data) || $.parseJSON(data);
+                    console.log(obj);
+                    // get poswords
+                    var poswords = [];
+                    if (obj.hasOwnProperty("poswords")) {
+                        poswords = obj["poswords"];
+                    }
+                    // get poswords
+                    var negwords = [];
+                    if (obj.hasOwnProperty("negwords")) {
+                        negwords = obj["negwords"];
+                    }
+                    // get matches
+                    var matches = [];
+                    if (obj.hasOwnProperty("matches")) {
+                        doc_matches = obj["matches"];
+                        for (var docname in doc_matches) {
+                            if (doc_matches.hasOwnProperty(docname)) {
+                                // create document section
+                                var li = $('<li class="uk-open"><h3 class="uk-accordion-title">'+docname+'</h3></li>');
+                                // create matches section
+                                word_matches = doc_matches[docname];
+                                var accordion_content = $('<div class="uk-accordion-content"></div>');
+                                for (var match in word_matches) {
+                                    console.log(word_matches[match]);
+                                    var result = word_matches[match];
+                                    var paragraph = $('<p class="document-result">'+result.context.split(' ').map(function(x){return "<word>"+x+"</word>";}).join('')+'</p>');
+                                    // find center match string and surrounded text
+                                    var matched = paragraph.find(":contains('"+result.match+"')");
+                                    var prev = matched.prev();
+                                    var next = matched.next();
+                                    // get textwindows text as context
+                                    var context = [];
+                                    var prev_context = [];
+                                    var next_context = [];
+                                    for (i = 0; prev.text()!=''; i++) {
+                                        if (i < 10) {
+                                            context.unshift(prev.text());
+                                        } else {
+                                            prev_context.unshift(prev.text());
+                                        }
+                                        prev = prev.prev();
+                                    }
+                                    context.push(matched.text());
+                                    for (i = 0; next.text()!=''; i++) {
+                                        if (i < 5) {
+                                            context.push(next.text());
+                                        } else {
+                                            next_context.push(next.text());
+                                        }
+                                        next = next.next();
+                                    }
+                                    // hightlight textwindow
+                                    context = $('<span class="textwindow" style="background-color: #fff2ba;">'+context.join(' ')+'</span>');
+                                    // hightlight positive words
+                                    for (var index in poswords) {
+                                        var search_regexp = new RegExp(poswords[index], "g");
+                                        context.html(context.html().replace(search_regexp,"<span style='background: #a5ffbf;' class='positive'>"+poswords[index]+"</span>"));
+                                    }
+                                    // hightlight acknowledgment keywords
+                                    if (result.hasOwnProperty("acknmatch")) {
+                                        var acknmatches = result["acknmatch"];
+                                        for (var index in acknmatches) {
+                                            var search_regexp = new RegExp(acknmatches[index], "g");
+                                            context.html(context.html().replace(search_regexp,"<span style='background: #a5ffbf;' class='positive'>"+acknmatches[index]+"</span>"));
+                                        }
+                                    }
+                                    // hightlight negative words
+                                    for (var index in negwords) {
+                                        var search_regexp = new RegExp(negwords[index], "g");
+                                        context.html(context.html().replace(search_regexp,"<span style='background: #ffc5c5;' class='negative'>"+negwords[index]+"</span>"));
+                                    }
+                                    // hightlight matched phrase
+                                    var search_regexp = new RegExp(result.match, "g");
+                                    context.html(context.html().replace(search_regexp,"<span style='background: #aee4f7;' class='highlight'><b>"+result.match+"</b></span>"));
+
+                                    // construct results paragraph to show
+                                    paragraph = $('<p class="document-result">'+prev_context.join(' ')+' '+context[0].outerHTML+' '+next_context.join(' ')+'</p>');
+
+                                    li.append(paragraph);
+                                }
+                                $("#docs-results").append(li);
+                            }
+                        }
+                        UIkit.accordion($("#docs-results"));
+                    }
+                    $("#results-section").show();
+                    // split all paragraphs to word spans
+                    // $(".document-result").each(function() {
+                    //     $(this).html($( this ).text().split(' ').map(function(x){return "<word>"+x+" </word>";}).join(''));
+                    //     var search_regexp = new RegExp("dolor", "g");
+                    //     $(this).html($(this).html().replace(search_regexp,"<span style='background: #c7ecc7;' class='highlight'>"+"AAAAAAAAA"+"</span>"));
+                    //     var matched = $(this).find(".highlight").parent();
+                    //     var prev = matched.prev();
+                    //     var next = matched.next();
+                    //     matched.css("background-color", "#fff2ba");
+                    //     // hightlight all prev window words
+                    //     for (i = 0; i < 3; i++) {
+                    //         prev.css("background-color", "#fff2ba");
+                    //         prev = prev.prev();
+                    //     }
+                    //     // hightlight all next window words
+                    //     for (i = 0; i < 3; i++) {
+                    //         next.css("background-color", "#fff2ba");
+                    //         next = next.next();
+                    //     }
+                    // });
                 },
                 error: function (xhr, ajaxOptions, thrownError) {
                   $('#file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
@@ -361,17 +559,29 @@
         });
     }
 
+    var uploadedDocs = 0
+
     var docsUploaded = function(docsNumber) {
+        uploadedDocs = docsNumber;
         $("#docs-number").html(docsNumber+" documents uploaded");
+    }
+
+    var hideInitialDocsUploadForm = function() {
+        console.log("AAAAAAAAA")
         $("#docs-more-btn").show();
-        $("#run-mining-btn").removeAttr("disabled");
+        $("#run-mining-btn").removeAttr('disabled').removeClass('disabled');
+        $('#documents-change-btn').addClass("uk-button");
+        $('#initial-docs-upload-form').attr("class", "");
+        $('#initial-docs-upload-form').attr("uk-dropdown", "mode: click;");
+        $('#initial-docs-upload-form').appendTo("#documents-section");
+        UIkit.dropdown($("#initial-docs-upload-form"));
+        UIkit.dropdown($("#initial-docs-upload-form")).mode = "click";
         handleRunMiningButton();
     }
 
     var handleFileUploadInput = function() {
         $("#docs-file-input").on('change', function() {
             if ($('#docs-file-input')[0].value === "") {
-              window.alert("You must specify a data file to upload.");
               return false;
             }
             // var formData = new FormData();
@@ -383,17 +593,16 @@
                 data: formData,
                 async: false,
                 success: function (data) {
-                    // TODO check for error
-                    $('#codes-file-upload-response').html(JSON.parse(data).respond)
+// TODO TODO TODO TODO TODO TODO check for error
                     obj = JSON && JSON.parse(data).data || $.parseJSON(data).data;
                     // console.log(obj);
-                    for (var key1 in obj) {
-                        if (obj.hasOwnProperty(key1)) {
-                          addDataToTable(generateId(), key1, obj[key1]);
+                    if (obj > 0) {
+                        if (uploadedDocs == 0) {
+                            hideInitialDocsUploadForm();
                         }
+                        docsUploaded(obj);
+                        UIkit.dropdown($("#initial-docs-upload-form")).hide();
                     }
-                    hideInitialDocsUploadForm();
-                    docsUploaded(12);
                 },
                 error: function (xhr, ajaxOptions, thrownError) {
                   $('#codes-file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
@@ -403,6 +612,7 @@
                 contentType: false,
                 processData: false
             });
+            $("#docs-file-input")[0].value = "";
 
             return false;
         });
@@ -411,7 +621,7 @@
     var handleDocSampleChoice = function(btnIndex) {
         var formData = new FormData();
         if (btnIndex === 0) {
-            formData.append("doc_sample", "nih_sample");
+            formData.append("doc_sample", "egi_sample");
         } else if (btnIndex === 1) {
             formData.append("doc_sample", "rcuk_sample");
         } else if (btnIndex === 2) {
@@ -425,17 +635,15 @@
             data: formData,
             async: false,
             success: function (data) {
-                // TODO check for error
-                $('#codes-file-upload-response').html(JSON.parse(data).respond)
+// TODO TODO TODO TODO TODO TODOcheck for error
                 obj = JSON && JSON.parse(data).data || $.parseJSON(data).data;
-                // console.log(obj);
-                for (var key1 in obj) {
-                    if (obj.hasOwnProperty(key1)) {
-                      addDataToTable(generateId(), key1, obj[key1]);
+                if (obj > 0) {
+                    if (uploadedDocs == 0) {
+                        hideInitialDocsUploadForm();
                     }
+                    docsUploaded(obj);
+                    UIkit.dropdown($("#initial-docs-upload-form")).hide();
                 }
-                hideInitialDocsUploadForm();
-                docsUploaded(12);
             },
             error: function (xhr, ajaxOptions, thrownError) {
               $('#codes-file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
@@ -450,7 +658,7 @@
     }
 
     var handleDocSampleButtons = function() {
-        $('#nih-sample').on('click', function( e ) {
+        $('#egi-sample').on('click', function( e ) {
             handleDocSampleChoice(0);
         });
         $('#rcuk-sample').on('click', function( e ) {
@@ -461,20 +669,137 @@
         });
     }
 
-    var hideInitialDocsUploadForm = function() {
-        $('#initial-docs-upload-form').hide();
+    var handleSaveProfileInfoSend = function() {
+        var formData = new FormData();
+        formData.append("createprofile", "1")
+        formData.append("poswords", JSON.stringify(wordsDataToArray(1)));
+        formData.append("negwords", JSON.stringify(wordsDataToArray(0)));
+        filters_list = {};
+        filters_list["lettercase"] = $("#letter-case-select option:selected").text();
+        filters_list["wordssplitnum"] = $("#word-split").val();
+        filters_list["stopwords"] = $('#stop-words-filter').prop('checked')===true?1:0;
+        filters_list["punctuation"] = $('#punctuation-filter').prop('checked')===true?1:0;
+        formData.append("filters", JSON.stringify(filters_list));
+        $.ajax({
+            url: "save-profile",
+            type: 'POST',
+            data: formData,
+            async: false,
+            success: function (data) {
+                console.log(data)
+                // if (data.indexOf('successfully!') != -1) {
+                //   $('#file-uploaded')[0].checked = true;
+                // }
+                window.location="save-profile"
+            },
+            error: function (xhr, ajaxOptions, thrownError) {
+              $('#file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
+              // $('#file-uploaded')[0].checked = false;
+            },
+            cache: false,
+            contentType: false,
+            processData: false
+        });
+    }
+
+    var handleSaveProfileButtons = function() {
+        $("#next-button").on('click', function(e) {
+            handleSaveProfileInfoSend();
+        });
+        $("#save-profile-option").on('click', function(e) {
+            handleSaveProfileInfoSend();
+        });
+    }
+
+    var checkAlreadyUploadedDocs = function() {
+      var formData = new FormData();
+      formData.append("already", "");
+      $.ajax({
+          url: "configure-profile",
+          type: 'POST',
+          data: formData,
+          async: false,
+          success: function (data) {
+              obj = JSON && JSON.parse(data).data || $.parseJSON(data).data;
+              console.log(data);
+              if (obj > 0) {
+                hideInitialDocsUploadForm();
+                docsUploaded(obj);
+              } else if (obj == -1) {
+                localStorage.clear();
+              }
+              init();
+          },
+          error: function (xhr, ajaxOptions, thrownError) {
+            $('#codes-file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
+            // $('#file-uploaded')[0].checked = false;
+          },
+          cache: false,
+          contentType: false,
+          processData: false
+      });
+    }
+
+    var checkAlreadyMiningSettings = function() {
+        for (var key in localStorage) {
+          if (key === null)
+            continue;
+          var value = localStorage.getItem(key);
+            console.log(key+' '+value);
+          if(key.indexOf('positive') === 0){
+            data = JSON.parse(value);
+            addDataToTable(key, data.phrase, data.weight, 1);
+          } else if(key.indexOf('negative') === 0) {
+            data = JSON.parse(value);
+            addDataToTable(key, data.phrase, data.weight, 0);
+          } else if (key === 'matchlevel') {
+            console.log(key+' '+value);
+            $(value).click();
+          } else if (key === 'lettercase') {
+            $("#letter-case-select").val(value);
+          } else if (key === 'wordssplitnum') {
+            $("#word-split").val(value)
+          } else if (key === 'stopwords') {
+            if (value == 1) {
+                $("#stop-words-filter").prop('checked', true);
+                $("#stop-words-filter").attr('checked', true);
+                $('#stop-words-filter')[0].checked = true;
+            } else if (value == 0) {
+                $("#stop-words-filter").prop('checked', false);
+                $("#stop-words-filter").attr('checked', false);
+                $('#stop-words-filter')[0].checked = false;
+                $('#stop-words-filter').removeAttr('checked');
+            }
+          } else if (key === 'punctuation') {
+            if (value == 1) {
+                $("#punctuation-filter").prop('checked', true);
+                $("#punctuation-filter").attr('checked', true);
+                $('#punctuation-filter')[0].checked = true;
+            } else if (value == 0) {
+                $("#punctuation-filter").prop('checked', false);
+                $("#punctuation-filter").attr('checked', false);
+                $('#punctuation-filter')[0].checked = false;
+                $('#punctuation-filter').removeAttr('checked');
+            }
+          }
+        }
+        if (localStorage.getItem('matchlevel') === null) {
+            // Click the by default option
+            $('#1-level').click();
+        }
     }
 
     var init = function(){
-        localStorage.clear();
         handleMatchLevelChoice();
+        checkAlreadyMiningSettings();
         handleWordsInput();
+        handleFiltersInput();
         handleDocSampleButtons();
         handleFileUploadInput();
-        handleNextButton();
+        handleSaveProfileButtons();
     };
 
     //start all
-    init();
+    checkAlreadyUploadedDocs();
 
 })();
diff --git a/interactive-mining-madoap/madoap/src/static/egi_sample.tsv b/interactive-mining-madoap/madoap/src/static/egi_sample.tsv
new file mode 100644
index 0000000..d47942c
--- /dev/null
+++ b/interactive-mining-madoap/madoap/src/static/egi_sample.tsv
@@ -0,0 +1 @@
+{"id":"atlasDoc", "text":"The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from CERN and the ATLAS Collaboration."}
\ No newline at end of file
diff --git a/interactive-mining-madoap/madoap/src/static/save-profile.js b/interactive-mining-madoap/madoap/src/static/save-profile.js
new file mode 100644
index 0000000..e3fcbe1
--- /dev/null
+++ b/interactive-mining-madoap/madoap/src/static/save-profile.js
@@ -0,0 +1,15 @@
+(function(){
+
+    function getCookie(name) {
+        var value = "; " + document.cookie;
+        var parts = value.split("; " + name + "=");
+        if (parts.length == 2) return parts.pop().split(";").shift();
+    }
+
+    var init = function(){
+    };
+
+    //start all
+    init();
+
+})();
diff --git a/interactive-mining-madoap/madoap/src/static/upload-codes.js b/interactive-mining-madoap/madoap/src/static/upload-codes.js
index 3e1d9d3..772f79a 100644
--- a/interactive-mining-madoap/madoap/src/static/upload-codes.js
+++ b/interactive-mining-madoap/madoap/src/static/upload-codes.js
@@ -41,7 +41,7 @@
 
     var onUserStartTyping = function() {
         $("#initial-type-input").on( 'keypress', function( e ){
-            $(this).css('display', 'none');
+            triggerDataTable();
             var value = $(this).val();
             var newId = generateId();
             addDataToTable(newId, value, "");
@@ -52,7 +52,10 @@
 
     var handleAddRowButton = function() {
         $('#add-row-below').on('click', function( e ) {
-            addDataToTable(generateId(), "", "");
+            var newId = generateId();
+            addDataToTable(newId, "", "");
+            var currentEle = $('#'+ newId).find("td.code");
+            editValue(currentEle, " ", 0);
         });
     }
 
@@ -88,6 +91,8 @@
             // $(this).children('td').each(function(ii, vv){
             //     data[i][ii] = $(this).text();
             // });
+            if ($(v).find("td.code").text() === '')
+              return true;
             data[$(v).find("td.code").text()] = $(v).find("td.acknowl").text();
         })
         return data
@@ -148,17 +153,27 @@
 
     var removeDataRow = function(id){
       var item = $('#' + id );
-      
+    
       item.addClass('removed-item')
           .one('webkitAnimationEnd oanimationend msAnimationEnd animationend', function(e) {
               $(this).remove();
+              // fix # column numbering
+              count_table_rows = 1;
+              $("#data-table tbody tr").each(function(i, v){
+                // data[i] = Array();
+                // $(this).children('td').each(function(ii, vv){
+                //     data[i][ii] = $(this).text();
+                // });
+                $(v).find("td.num").text(count_table_rows);
+                count_table_rows++;
+              })
            });
     };
 
     var count_table_rows = 1;
 
     var addDataToTable = function(id, code, acknowledgment) {
-        var row = '<tr id="' + id + '"><td>'+count_table_rows+'</td><td class="code">' + code + '</td><td class="acknowl">' + acknowledgment +'</td></tr>'
+        var row = '<tr id="' + id + '"><td class="num">'+count_table_rows+'</td><td class="code">' + code + '</td><td class="acknowl">' + acknowledgment +'</td></tr>'
         table = $('#data-table tbody');
 
         // if content is correct and not empty append to table
@@ -187,8 +202,13 @@
         });
     }
 
+    var triggerDataTable = function() {
+      $("#initial-type-input").remove();
+      $("#data-table").show();
+    }
+
     var handleFileUploadButton = function() {
-        $("form#codes-file-input-form").submit(function(){
+        $("form#codes-file-input-form").on('change', function(){
             if ($('#codes-file-input')[0].value === "") {
               window.alert("You must specify a data file to import.");
               return false;
@@ -209,6 +229,7 @@
                           addDataToTable(generateId(), key1, obj[key1]);
                         }
                     }
+                    triggerDataTable();
                 },
                 error: function (xhr, ajaxOptions, thrownError) {
                   $('#codes-file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
@@ -223,8 +244,40 @@
         });
     }
 
+    var checkAlreadyUserState = function() {
+      var formData = new FormData();
+      formData.append("already", "");
+      $.ajax({
+          url: "upload-codes",
+          type: 'POST',
+          data: formData,
+          async: false,
+          success: function (data) {
+              obj = JSON && JSON.parse(data).data || $.parseJSON(data).data;
+              // console.log(obj);
+              var numOfCodes = 0;
+              for (var key1 in obj) {
+                  if (obj.hasOwnProperty(key1)) {
+                    addDataToTable(generateId(), key1, obj[key1]);
+                  }
+                  numOfCodes++
+              }
+              if (numOfCodes != 0) {
+                triggerDataTable();
+              }
+          },
+          error: function (xhr, ajaxOptions, thrownError) {
+            $('#codes-file-upload-response').html('<b style=\"color: red\">File Failed to Upload!</b>'+xhr.status)
+            // $('#file-uploaded')[0].checked = false;
+          },
+          cache: false,
+          contentType: false,
+          processData: false
+      });
+    }
+
     var init = function(){
-        localStorage.clear();
+        checkAlreadyUserState();
         handleFileUploadButton();
         onUserStartTyping();
         handleAddRowButton();
diff --git a/interactive-mining-madoap/madoap/src/templates/configure_profile.html b/interactive-mining-madoap/madoap/src/templates/configure_profile.html
index d146837..8db2f3d 100644
--- a/interactive-mining-madoap/madoap/src/templates/configure_profile.html
+++ b/interactive-mining-madoap/madoap/src/templates/configure_profile.html
@@ -2,17 +2,18 @@
 {% block configure_profile %} class="current" {% end %}
 {% block content %}
 <title>Configure profile</title>
+<link rel="stylesheet" href="/static/animations.css"/>
 
-<button class="uk-close-large" type="button" uk-close></button>
+<a href="/"><button id="cancel-main-btn" class="uk-close-large" type="button" uk-close></button></a>
 <div class="uk-container tm-toolbar custom-discover-toolbar uk-visible@m uk-container-small">
     <div class="uk-flex uk-flex-middle">
         <div class="uk-margin-auto-right">
             <div class="uk-grid-medium uk-child-width-auto uk-flex-middle uk-grid uk-grid-stack" uk-grid="margin: uk-margin-small-top">
                 <div class="uk-first-column">
                     <ul class="uk-subnav uk-subnav-line">
-                        <li><a href="#">Upload your project codes</a></li>
-                        <li class="custom-discover-li"><a class="router-link-active" href="#">Configure the matching proccess</a></li>
-                        <li><a href="#">Save matching profile</a></li>
+                        <li><a href="upload-codes">Upload your project codes</a></li>
+                        <li class="custom-discover-li"><a class="router-link-active" href="configure-profile">Configure the matching proccess</a></li>
+                        <li><a id="save-profile-option">Save matching profile</a></li>
                     </ul>
                 </div>
             </div>
@@ -48,7 +49,7 @@
                     </div>
                 </div>
                 <hr>
-                <ul uk-accordion id="uk-accordion">
+                <ul uk-accordion id="advanced-opts-toggle">
                     <li>
                         <h5 class="uk-accordion-title">Advance tools <span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h5>
                         <div class="uk-accordion-content">
@@ -77,8 +78,8 @@
                                                     </tbody>
                                                 </table>
                                                 <footer>
-                                                    <span class="count" id="count-pos"></span>
-                                                    <button class="btn clear-all" id="clear-all-pos">Delete All</button>
+                                                    <span class="count" id="count-pos">0</span>
+                                                    <button class="uk-button uk-button-default" disabled id="clear-all-pos">Delete All</button>
                                                 </footer>
                                             </div>
                                         </div>
@@ -104,8 +105,8 @@
                                                     </tbody>
                                                 </table>
                                                 <footer>
-                                                    <span class="count" id="count-neg"></span>
-                                                    <button class="btn clear-all" id="clear-all-neg">Delete All</button>
+                                                    <span class="count" id="count-neg">0</span>
+                                                    <button class="uk-button uk-button-default" disabled id="clear-all-neg">Delete All</button>
                                                 </footer>
                                             </div>
                                         </div>
@@ -122,12 +123,21 @@
                             <div class="uk-section uk-section-default">
                                 <div class="uk-container">
                                     <h5>Clean matching area's text<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h5>
-                                    <div class="uk-margin uk-grid-small uk-child-width-auto" uk-grid>
-                                        <label>N-grams length<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span><input type="number" name="word-split" min="0" max="10" id="word-split" placeholder="Word pairs" value="2"/></label>
-                                        <label><input id="stop-words-filter" class="uk-checkbox" type="checkbox" checked> Remove stop words<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
-                                        <label><input id="punctuation-filter" class="uk-checkbox" type="checkbox"> Remove punctuation<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
-                                        <form class="uk-form-horizontal">
-                                            <label class="uk-form-label" for="letter-case-select">Letter case convertion to<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
+                                    <form class="uk-form-stacked">
+                                        <div class="uk-margin">
+                                            <label class="uk-form-label" for="word-split">N-grams length <span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
+                                            <div class="uk-form-controls">
+                                                <input class="uk-input" type="number" name="word-split" min="0" max="10" id="word-split" placeholder="Word pairs" value="2"/>
+                                            </div>
+                                        </div>
+                                        <div class="uk-margin">
+                                            <label class="uk-form-label" for="stop-words-filter"><input id="stop-words-filter" class="uk-checkbox" type="checkbox"> Remove stop words <span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
+                                        </div>
+                                        <div class="uk-margin">
+                                            <label class="uk-form-label" for="punctuation-filter"><input id="punctuation-filter" class="uk-checkbox" type="checkbox"> Remove punctuation <span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
+                                        </div>
+                                        <div class="uk-margin">
+                                            <label class="uk-form-label" for="letter-case-select">Letter case convertion to <span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></label>
                                             <div class="uk-form-controls">
                                                 <select class="uk-select" id="letter-case-select">
                                                     <option>None</option>
@@ -135,9 +145,8 @@
                                                     <option>Uppercase</option>
                                                 </select>
                                             </div>
-                                        </form>
-                                        
-                                    </div>
+                                        </div>
+                                    </form>
                                 </div>
                             </div>
                         </div>
@@ -150,8 +159,8 @@
                         <div>
                             <h4>Matching results<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h4>
                         </div>
-                        <div>
-                            <div class="uk-float-right">
+                        <div id="documents-section" class="uk-inline">
+                            <div id="documents-change-btn" class="uk-float-right">
                                 <span id="docs-number" class="uk-text">0 documents uploaded</span>
                                 <span id="docs-more-btn" class="uk-margin-small-left" uk-icon="icon: more" style="display: none;"></span>
                             </div>
@@ -159,43 +168,40 @@
                     </div>
                     <button id="run-mining-btn" class="uk-button uk-button-primary uk-margin-top" disabled>Run mining</button>
                 </div>
-                <div id="initial-docs-upload-form" class="uk-section uk-section-muted uk-margin-top uk-padding">
-                    <div class="uk-container">
-                        <div class="uk-alert-danger" uk-alert>
-                            <a class="uk-alert-close" uk-close></a>
-                            <p>No documents to test matching accuracy.</p>
-                        </div>
-                        <h4>Choose a sample of documents to load<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h4>
-                        <div class="uk-text-center">
-                            <button id="nih-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">NIH documents</button>
-                            <button id="rcuk-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">RCUK documents</button>
-                            <button id="arxiv-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">ARXIV documents</button>
-                        </div>
-                        <h4>Upload your project codes you want to match<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h4>
-                        <div class="test-upload uk-placeholder uk-text-center">
-                            <p><span uk-icon="icon: upload; ratio: 3.5"></span></p>
-                            <p>
-                                <span class="uk-text-middle">Attach documents file by dropping them here or</span>
-                                <div uk-form-custom>
-                                    <form id="docs-input-form" method="post" enctype="multipart/form-data" accept-charset="UTF-8">
-                                        <input type="file" name="upload" id="docs-file-input" class="inputfile">
-                                    </form>
-                                    <span class="uk-link">browse documents file</span>
-                                </div>
-                            </p>
-                            <p>
-                                <span class="uk-label uk-margin-small-right">JSON</span><span class="uk-label uk-margin-small-right">PDF</span><span class="uk-label">TXT</span>
-                                <span class="uk-text">file types</span>
-                            </p>
-                            <p class="uk-text-middle">Maximum 10MB upload</p>
-                        </div>
+                <div id="initial-docs-upload-form" class="uk-card uk-card-default uk-card-large uk-card-body">
+                    <h4>Choose a sample of documents to load<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h4>
+                    <div class="uk-text-center">
+                        <button id="egi-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">EGI documents</button>
+                        <button id="rcuk-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">RCUK documents</button>
+                        <button id="arxiv-sample" class="uk-button uk-width-large uk-button-primary uk-margin-small">ARXIV documents</button>
+                    </div>
+                    <h4>Upload your project codes you want to match<span uk-icon="icon: info" title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom"></span></h4>
+                    <div class="test-upload uk-placeholder uk-text-center">
+                        <p><span uk-icon="icon: upload; ratio: 3.5"></span></p>
+                        <p>
+                            <span class="uk-text-middle">Attach documents file by dropping them here or</span>
+                            <div uk-form-custom>
+                                <form id="docs-input-form" method="post" enctype="multipart/form-data" accept-charset="UTF-8">
+                                    <input type="file" name="upload" id="docs-file-input" class="inputfile">
+                                </form>
+                                <span class="uk-link">browse documents file</span>
+                            </div>
+                        </p>
+                        <p>
+                            <span class="uk-label uk-margin-small-right">JSON</span><span class="uk-label uk-margin-small-right">PDF</span><span class="uk-label">TXT</span>
+                            <span class="uk-text">file types</span>
+                        </p>
+                        <p class="uk-text-middle">Maximum 10MB upload</p>
                     </div>
                 </div>
                 <div id="results-section" class="uk-section uk-section-default" style="display: none;">
-                    <div class="uk-container">
-
+                    <div class="uk-container" style="overflow: auto; -webkit-overflow-scrolling: touch; max-height: 600px;">
+                        <ul id="docs-results" uk-accordion="multiple: true">
+                            
+                        </ul>
                     </div>
                 </div>
+                <button id="next-button" class="uk-button uk-button-primary uk-margin-top uk-margin-right uk-float-right">Next</button>
             </div>
         </div>
     </div>
diff --git a/interactive-mining-madoap/madoap/src/templates/save_profile.html b/interactive-mining-madoap/madoap/src/templates/save_profile.html
index 4e33ac5..71ac3c8 100644
--- a/interactive-mining-madoap/madoap/src/templates/save_profile.html
+++ b/interactive-mining-madoap/madoap/src/templates/save_profile.html
@@ -3,16 +3,16 @@
 {% block content %}
 <title>Save profile</title>
 
-<button class="uk-close-large" type="button" uk-close></button>
+<a href="/"><button id="cancel-main-btn" class="uk-close-large" type="button" uk-close></button></a>
 <div class="uk-container tm-toolbar custom-discover-toolbar uk-visible@m uk-container-small">
     <div class="uk-flex uk-flex-middle">
         <div class="uk-margin-auto-right">
             <div class="uk-grid-medium uk-child-width-auto uk-flex-middle uk-grid uk-grid-stack" uk-grid="margin: uk-margin-small-top">
                 <div class="uk-first-column">
                     <ul class="uk-subnav uk-subnav-line">
-                        <li><a href="#">Upload your project codes</a></li>
-                        <li><a href="#">Configure the matching proccess</a></li>
-                        <li class="custom-discover-li"><a class="router-link-active" href="#">Save matching profile</a></li>
+                        <li><a href="upload-codes">Upload your project codes</a></li>
+                        <li><a href="configure-profile">Configure the matching proccess</a></li>
+                        <li class="custom-discover-li"><a class="router-link-active" href="save-profile">Save matching profile</a></li>
                     </ul>
                 </div>
             </div>
@@ -23,10 +23,10 @@
 <div class="uk-section uk-section-default">
     <div class="uk-container uk-container-small">
 
-		<div class="test-upload uk-button uk-button-default uk-width-1-1 uk-button-large uk-text-center">
+		<a id="save-profile-btn" class="test-upload uk-button uk-button-default uk-width-1-1 uk-button-large uk-text-center" href="save-profile?saveprofile=1">
 		    <span uk-icon="icon: download"></span>
 		    <span class="uk-text-middle">Download profile</span>
-		</div>
+		</a>
 		<div class="uk-heading-line uk-text-center uk-margin-small-top uk-margin-small-bottom"><span>or</span></div>
 		<div class="test-upload uk-button uk-button-link uk-width-1-1 uk-text-center">
 		    <span class="uk-text-middle">LOGIN to save your profile</span>
@@ -34,4 +34,5 @@
 	</div>
 </div>
 
+<script src="/static/save-profile.js" type="text/javascript"></script>
 {% end %}
\ No newline at end of file
diff --git a/interactive-mining-madoap/madoap/src/templates/upload_codes.html b/interactive-mining-madoap/madoap/src/templates/upload_codes.html
index 42bea92..c7f23a3 100644
--- a/interactive-mining-madoap/madoap/src/templates/upload_codes.html
+++ b/interactive-mining-madoap/madoap/src/templates/upload_codes.html
@@ -2,17 +2,18 @@
 {% block upload_codes %} class="current" {% end %}
 {% block content %}
 <title>Upload project codes</title>
+<link rel="stylesheet" href="/static/animations.css"/>
 
-<button class="uk-close-large" id="cancel-proccess-btn" type="button" uk-close></button>
+<a href="/"><button id="cancel-main-btn" class="uk-close-large" type="button" uk-close></button></a>
 <div class="uk-container tm-toolbar custom-discover-toolbar uk-visible@m uk-container-small">
     <div class="uk-flex uk-flex-middle">
         <div class="uk-margin-auto-right">
             <div class="uk-grid-medium uk-child-width-auto uk-flex-middle uk-grid uk-grid-stack" uk-grid="margin: uk-margin-small-top">
                 <div class="uk-first-column">
                     <ul class="uk-subnav uk-subnav-line">
-                        <li class="custom-discover-li"><a href="#" class="router-link-active">Upload your project codes</a></li>
-                        <li><a href="#">Configure the matching proccess</a></li>
-                        <li><a href="#">Save matching profile</a></li>
+                        <li class="custom-discover-li"><a href="upload-codes" class="router-link-active">Upload your project codes</a></li>
+                        <li><a href="configure-profile">Configure the matching proccess</a></li>
+                        <li><a>Save matching profile</a></li>
                     </ul>
                 </div>
             </div>
@@ -23,19 +24,14 @@
 <div class="uk-container uk-container-small">
     <h4>Upload your project codes you want to match <span title="If you want the tooltip to appear with a little delay, just add the delay option to the uk-tooltip attribute with your value in milliseconds." uk-tooltip="pos: bottom" uk-icon="icon: info"></span></h4>
 
-    <div class="file-upload-wrapper js">
-        <form id="codes-file-input-form" method="post" enctype="multipart/form-data" accept-charset="UTF-8">
-            <header>
+    <form id="codes-file-input-form" method="post" enctype="multipart/form-data" accept-charset="UTF-8">
+        <div class="uk-margin">
+            <div uk-form-custom>
                 <input type="file" name="upload" id="codes-file-input" class="inputfile" />
-                <label for="codes-file-input" id="codes-file-input-label" ><strong><svg xmlns="http://www.w3.org/2000/svg" width="20" height="17" viewBox="0 0 20 17"><path d="M10 0l-5.2 4.9h3.3v5.1h3.8v-5.1h3.3l-5.2-4.9zm9.3 11.5l-3.2-2.1h-2l3.4 2.6h-3.5c-.1 0-.2.1-.2.1l-.8 2.3h-6l-.8-2.2c-.1-.1-.1-.2-.2-.2h-3.6l3.4-2.6h-2l-3.2 2.1c-.4.3-.7 1-.6 1.5l.6 3.1c.1.5.7.9 1.2.9h16.3c.6 0 1.1-.4 1.3-.9l.6-3.1c.1-.5-.2-1.2-.7-1.5z"/></svg> Choose a file&hellip;</strong> <span id="codes-file-title-text"></span></label>
-                <button id="upload-button" class="btn" style="float: right; margin-right: 5px;" >Upload</button>
-            </header>
-            <footer>
-                <span class="response" id="codes-file-upload-response">
-                </span>
-            </footer>
-        </form>
-    </div>
+                <strong><svg xmlns="http://www.w3.org/2000/svg" width="20" height="17" viewBox="0 0 20 17"><path d="M10 0l-5.2 4.9h3.3v5.1h3.8v-5.1h3.3l-5.2-4.9zm9.3 11.5l-3.2-2.1h-2l3.4 2.6h-3.5c-.1 0-.2.1-.2.1l-.8 2.3h-6l-.8-2.2c-.1-.1-.1-.2-.2-.2h-3.6l3.4-2.6h-2l-3.2 2.1c-.4.3-.7 1-.6 1.5l.6 3.1c.1.5.7.9 1.2.9h16.3c.6 0 1.1-.4 1.3-.9l.6-3.1c.1-.5-.2-1.2-.7-1.5z"/></svg> Choose a file&hellip;</strong>
+            </div>
+        </div>
+    </form>
 
 <!--     <div class="test-upload uk-placeholder uk-text-center">
         <p><span uk-icon="icon: upload; ratio: 3.5"></span></p>
@@ -55,7 +51,7 @@
 
     <input id="initial-type-input" class="uk-input uk-form-width-medium uk-form-large uk-width-1-1 uk-text-center" type="text" placeholder="Start typing project or Paste">
 
-    <table id="data-table" class="uk-table uk-table-divider .uk-table-striped uk-table-hover">
+    <table id="data-table" class="uk-table uk-table-divider .uk-table-striped uk-table-hover" style="display: none;">
         <thead>
             <tr>
                 <th class="uk-table-shrink">#</th>