Merge branch 'testing' into prod-dev

parsing/FileParsers/EuropressFileParser.py

@@ -11,7 +11,7 @@ from ..NgramsExtractors import *
 from admin.utils import PrintException
 
 class EuropressFileParser(FileParser):
-  
+
     def _parse(self, file):
 
         localeEncoding = "fr_FR"
@@ -39,21 +39,21 @@ class EuropressFileParser(FileParser):
         try:
             html_parser = etree.HTMLParser(encoding=codif)
             html = etree.fromstring(contents, html_parser)
-            
+
             try :
-                
+
                 format_europresse = 50
                 html_articles = html.xpath('/html/body/table/tbody')
 
                 if len(html_articles) < 1:
                     html_articles = html.xpath('/html/body/table')
-                    
+
                     if len(html_articles) < 1:
                         format_europresse = 1
                         html_articles = html.xpath('//div[@id="docContain"]')
             except :
                 PrintException()
-            
+
             if format_europresse == 50 :
                 name_xpath      = "./tr/td/span[@class = 'DocPublicationName']"
                 header_xpath    = "./tr/td/span[@class = 'DocHeader']"
@@ -77,7 +77,7 @@ class EuropressFileParser(FileParser):
                         or self::td[@class='txtCertificat'] \
                         )]/text()"
                 doi_xpath  = "//span[@id='ucPubliC_lblNodoc']/text()"
-                
+
 
         except Exception as error :
             PrintException()
@@ -85,9 +85,9 @@ class EuropressFileParser(FileParser):
         # parse all the articles, one by one
         try:
             for html_article in html_articles:
-                
+
                 hyperdata = {}
-                
+
                 if len(html_article):
                     for name in html_article.xpath(name_xpath):
                         if name.text is not None:
@@ -98,26 +98,26 @@ class EuropressFileParser(FileParser):
                                 hyperdata['volume'] = test_journal.group(2)
                             else:
                                 hyperdata['journal'] = name.text.encode(codif)
-                    
+
                     countbis = 0
 
                     for header in html_article.xpath(header_xpath):
 #                        print(count)
 #                        countbis += 1
-                        
+
 #                        try:
 #                            print('109', hyperdata['publication_date'])
 #                        except:
 #                            print('no date yet')
 #                            pass
-                        
+
                         try:
                             text = header.text
                             #print("header", text)
                         except Exception as error:
                             print(error)
 
-                        
+
                         if isinstance(text, bytes):
                             text = text.decode(encoding)
                         format_date_fr = re.compile('\d*\s*\w+\s+\d{4}', re.UNICODE)
@@ -134,9 +134,9 @@ class EuropressFileParser(FileParser):
                             test_date_en = None
                             test_sect = None
                             test_page = None
-                        
-                        
-                        
+
+
+
                         if test_date_fr is not None:
                             self.localeEncoding = "fr_FR"
                             locale.setlocale(locale.LC_ALL, localeEncoding)
@@ -158,7 +158,7 @@ class EuropressFileParser(FileParser):
                                     except Exception as error:
                                         print(error, text)
                                         pass
-                        
+
 
                         if test_date_en is not None:
                             localeEncoding = "en_GB.UTF-8"
@@ -173,20 +173,20 @@ class EuropressFileParser(FileParser):
 
                         if test_sect is not None:
                             hyperdata['section'] = test_sect.group(1).encode(codif)
-                        
+
                         if test_page is not None:
                             hyperdata['page'] = test_page.group(1).encode(codif)
-                    
-                    try:
-                        print('183', hyperdata['publication_date'])
-                    except:
-                        print('no date yet')
-                        pass
-                        
+
+#                    try:
+#                        print('183', hyperdata['publication_date'])
+#                    except:
+#                        print('no date yet')
+#                        pass
+#
 
                     hyperdata['title'] = html_article.xpath(title_xpath).encode(codif)
                     hyperdata['abstract']  = html_article.xpath(text_xpath)
-                   
+
                     line = 0
                     br_tag = 10
                     for i in html_articles[count].iter():
@@ -205,13 +205,13 @@ class EuropressFileParser(FileParser):
                                 hyperdata['authors'] = 'not found'
                             line = 0
                             br_tag = 10
-                    
-                                       
+
+
                     try:
                         if hyperdata['publication_date'] is not None or hyperdata['publication_date'] != '':
                             try:
                                 back = hyperdata['publication_date']
-                            except Exception as e: 
+                            except Exception as e:
                                 #print(e)
                                 pass
                         else:
@@ -226,14 +226,14 @@ class EuropressFileParser(FileParser):
                     #hyperdata['language_iso2'] = 'fr'
                     #elif lang == 'en':
                     #    hyperdata['language_iso2'] = 'en'
-                    
-                    
+
+
                     hyperdata['publication_year']  = hyperdata['publication_date'].strftime('%Y')
                     hyperdata['publication_month'] = hyperdata['publication_date'].strftime('%m')
                     hyperdata['publication_day']  = hyperdata['publication_date'].strftime('%d')
                     #hyperdata.pop('publication_date')
-                    
-                    if len(hyperdata['abstract'])>0 and format_europresse == 50: 
+
+                    if len(hyperdata['abstract'])>0 and format_europresse == 50:
                         hyperdata['doi'] = str(hyperdata['abstract'][-9])
                         hyperdata['abstract'].pop()
 # Here add separator for paragraphs
@@ -245,15 +245,15 @@ class EuropressFileParser(FileParser):
 # Here add separator for paragraphs
                         hyperdata['abstract'] = str(' '.join(hyperdata['abstract']))
 
-                    else: 
+                    else:
                         hyperdata['doi'] = "not found"
-                    
+
                     hyperdata['length_words'] = len(hyperdata['abstract'].split(' '))
                     hyperdata['length_letters'] = len(hyperdata['abstract'])
-                    
+
                     hyperdata['bdd']  = u'europresse'
                     hyperdata['url']  = u''
-                    
+
                   #hyperdata_str = {}
                     for key, value in hyperdata.items():
                         hyperdata[key] = value.decode() if isinstance(value, bytes) else value

parsing/FileParsers/FileParser.py

@@ -4,21 +4,21 @@ import zipfile
 import chardet
 
 from ..Caches import LanguagesCache
-    
+
 
 class FileParser:
     """Base class for performing files parsing depending on their type.
     """
     def __init__(self, language_cache=None):
         self._languages_cache = LanguagesCache() if language_cache is None else language_cache
-    
+
     def detect_encoding(self, string):
         """Useful method to detect the document encoding.
         """
         encoding = chardet.detect(string)
         return encoding.get('encoding', 'UTF-8')
-    
-    
+
+
     def format_hyperdata_dates(self, hyperdata):
         """Format the dates found in the hyperdata.
         Examples:
@@ -27,7 +27,7 @@ class FileParser:
             {"publication_year": "2014"}
             -> {"publication_date": "2014-01-01 00:00:00", "publication_year": "2014", ...}
         """
-        
+
         # First, check the split dates...
         prefixes = [key[:-5] for key in hyperdata.keys() if key[-5:] == "_year"]
         for prefix in prefixes:
@@ -51,21 +51,23 @@ class FileParser:
                 hyperdata[prefix + "_date"] = dateutil.parser.parse(date_string).strftime("%Y-%m-%d %H:%M:%S")
             except:
                 pass
-        
+
         # ...then parse all the "date" fields, to parse it into separate elements
         prefixes = [key[:-5] for key in hyperdata.keys() if key[-5:] == "_date"]
         for prefix in prefixes:
             date = dateutil.parser.parse(hyperdata[prefix + "_date"])
+            print('date')
+
             hyperdata[prefix + "_year"]      = date.strftime("%Y")
             hyperdata[prefix + "_month"]     = date.strftime("%m")
             hyperdata[prefix + "_day"]       = date.strftime("%d")
             hyperdata[prefix + "_hour"]      = date.strftime("%H")
             hyperdata[prefix + "_minute"]    = date.strftime("%M")
             hyperdata[prefix + "_second"]    = date.strftime("%S")
-                
+
         # finally, return the transformed result!
         return hyperdata
-        
+
     def format_hyperdata_languages(self, hyperdata):
         """format the languages found in the hyperdata."""
         language = None
@@ -81,18 +83,18 @@ class FileParser:
             hyperdata["language_iso3"]       = language.iso3
             hyperdata["language_fullname"]   = language.fullname
         return hyperdata
-        
+
     def format_hyperdata(self, hyperdata):
         """Format the hyperdata."""
         hyperdata = self.format_hyperdata_dates(hyperdata)
         hyperdata = self.format_hyperdata_languages(hyperdata)
         return hyperdata
-    
-    
+
+
     def _parse(self, file):
         """This method shall be overriden by inherited classes."""
         return list()
-        
+
     def parse(self, file):
         """Parse the file, and its children files found in the file.
         """

parsing/FileParsers/RisFileParser.py

@@ -3,15 +3,17 @@ from .FileParser import FileParser
 
 from ..Caches import LanguagesCache
 
+from admin.utils import PrintException
+
 class RisFileParser(FileParser):
 
     def __init__(self, language_cache=None):
-        
+
         super(FileParser, self).__init__()
         self._languages_cache = LanguagesCache() if language_cache is None else language_cache
-        
+
         self._begin = 6
-        
+
         self._parameters = {
             b"ER":  {"type": "delimiter"},
             b"TI":  {"type": "hyperdata", "key": "title", "separator": " "},
@@ -24,7 +26,7 @@ class RisFileParser(FileParser):
             b"AB":  {"type": "hyperdata", "key": "abstract", "separator": " "},
             b"WC":  {"type": "hyperdata", "key": "fields"},
         }
-        
+
 
     def _parse(self, file):
         hyperdata = {}
@@ -57,5 +59,11 @@ class RisFileParser(FileParser):
                     print(error)
         # if a hyperdata object is left in memory, yield it as well
         if hyperdata:
+#            try:
+#                if hyperdata['date_to_parse']:
+#                    print(hyperdata['date_to_parse'])
+#            except:
+#                pass
+#
             #print(hyperdata['title'])
             yield hyperdata

parsing/FileParsers/ZoteroFileParser.py

+from .RisFileParser import RisFileParser
+
+from ..Caches import LanguagesCache
+
+class ZoteroFileParser(RisFileParser):
+    def __init__(self):
+        super(RisFileParser, self).__init__()
+
+        self._begin = 6
+
+        self._parameters = {
+            b"ER":  {"type": "delimiter"},
+            b"TI":  {"type": "hyperdata", "key": "title", "separator": " "},
+            b"AU":  {"type": "hyperdata", "key": "authors", "separator": ", "},
+            b"UR":  {"type": "hyperdata", "key": "doi"},
+            b"DA":  {"type": "hyperdata", "key": "publication_date"},
+            b"PY":  {"type": "hyperdata", "key": "publication_year"},
+            b"PD":  {"type": "hyperdata", "key": "publication_month"},
+            b"LA":  {"type": "hyperdata", "key": "language_iso2"},
+            b"AB":  {"type": "hyperdata", "key": "abstract", "separator": " "},
+            b"WC":  {"type": "hyperdata", "key": "fields"},
+        }
+

parsing/FileParsers/__init__.py

 from .RisFileParser import RisFileParser
 from .IsiFileParser import IsiFileParser
 from .JstorFileParser import JstorFileParser
+from .ZoteroFileParser import ZoteroFileParser
 from .PubmedFileParser import PubmedFileParser
 from .EuropressFileParser import EuropressFileParser
 from .ISText import ISText

parsing/corpustools.py

@@ -128,7 +128,7 @@ def parse_resources(corpus, user=None, user_id=None):
             nodes.append(node)
             #
             # TODO: mark node-resources associations as parsed
-            # 
+            #
     dbg.show('insert %d documents' % len(nodes))
     session.add_all(nodes)
     session.commit()
@@ -205,7 +205,7 @@ def extract_ngrams(corpus, keys):
         language.id: language.iso2
         for language in session.query(Language)
     }
-    
+
     ngrams_data = set()
     ngrams_language_data = set()
     ngrams_tag_data = set()
@@ -241,7 +241,7 @@ def extract_ngrams(corpus, keys):
                         #tag_id   =  14
                         #print('tag_id_2', tag_id)
                     node_ngram_list[node_id][terms] += 1
-                    ngrams_data.add((n, terms))
+                    ngrams_data.add((n, terms[:255]))
                     ngrams_language_data.add((terms, language_id))
                     ngrams_tag_data.add((terms, tag_id))
 
@@ -268,7 +268,7 @@ def extract_ngrams(corpus, keys):
             ngram.terms = tmp__ngrams.terms
     ''' % (Ngram.__table__.name, ))
     # insert, then get the ids back
-    
+
     cursor.execute('''
         INSERT INTO
             %s (n, terms)
@@ -279,8 +279,8 @@ def extract_ngrams(corpus, keys):
         WHERE
             id IS NULL
     ''' % (Ngram.__table__.name, ))
-    
-    
+
+
     cursor.execute('''
         UPDATE
             tmp__ngrams
@@ -293,14 +293,14 @@ def extract_ngrams(corpus, keys):
         AND
             tmp__ngrams.id IS NULL
     ''' % (Ngram.__table__.name, ))
-    
+
     # get all ids
     ngram_ids = dict()
     cursor.execute('SELECT id, terms FROM tmp__ngrams')
     for row in cursor.fetchall():
         ngram_ids[row[1]] = row[0]
-    
-    # 
+
+    #
     dbg.show('insert associations')
     node_ngram_data = list()
     for node_id, ngrams in node_ngram_list.items():

parsing/parsers_config.py

@@ -4,11 +4,11 @@ parsers = {
         'Pubmed (xml format)'               : PubmedFileParser,
         'Web of Science (ISI format)'       : IsiFileParser,
         'Scopus (RIS format)'               : RisFileParser,
-        'Zotero (RIS format)'               : JstorFileParser,
+        'Zotero (RIS format)'               : ZoteroFileParser,
         'Jstor (RIS format)'                : JstorFileParser,
         #'Europress'                        : EuropressFileParser,
         'Europress (French)'                : EuropressFileParser,
         'Europress (English)'               : EuropressFileParser,
-        
+
     }