Fix typos discover running harvester

controllers/harvest.py

@@ -9,20 +9,20 @@ from gluon import current
 from gluon.restricted import RestrictedError
 from harvest_tools import (build_harvester_tool,
                            CheckAndFix,
-                           CheckException,
                            DRY_RUN,
-                           MsgCollection,
-                           search_synonym,
-                           ToolException)
+                           MsgCollection)
 from plugin_dbui import (inline_alert,
                          Selector,
                          to_formPanel,
                          UNDEF_ID)
 from requests.exceptions import RequestException
-from store_tools import (load_record,
+from store_tools import (CheckException,
+                         load_record,
                          OAI_URL,
                          RecordCdsConfPaper,
-                         RecordCdsThesis)
+                         RecordCdsThesis,
+                         search_synonym,
+                         ToolException)
 
 MODE_DRY_RUN = T(DRY_RUN)
 MSG_GREMLIN = "Oops a gremlin..."

modules/harvest_tools/articles.py

@@ -65,8 +65,9 @@ class Articles(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/automaton.py

@@ -131,7 +131,7 @@ class Automaton(object):
         self.id_project = id_project
         self.logs = []
         self.logger = logging.getLogger("web2py.app.limbra")
-        self.rex_intitute = get_rex_institute(db, current.app)
+        self.rex_institute = get_rex_institute(db, current.app)
         self.store = None
         self.year_start = year_start
         self.year_end = year_end

modules/harvest_tools/base.py

@@ -138,6 +138,6 @@ def get_rex_institute(db, app):
 
             lst.append(val)
 
-        reg_institute = r"|".join(lst)
+        app.reg_institute = reg_institute = r"|".join(lst)
 
     return reg_institute

modules/harvest_tools/notes.py

@@ -45,8 +45,9 @@ class Notes(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/preprints.py

@@ -69,8 +69,9 @@ class Preprints(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/proceedings.py

@@ -51,8 +51,9 @@ class Proceedings(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/reports.py

@@ -45,8 +45,9 @@ class Reports(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/talks.py

@@ -50,8 +50,9 @@ class Talks(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/harvest_tools/thesis.py

@@ -42,8 +42,9 @@ class Thesis(Automaton):
             # format authors according to my format
             # extract authors form my institute signing the publication
             # is submitted date well formed
-            record.check_and_fix(self.rex_institute,
+            record.check_and_fix(db=self.db,
                                  fmt_author="F. Last",
+                                 rex_institute=self.rex_institute,
                                  sep_author=", ",
                                  sort_author=True)
 

modules/store_tools/recordcdspubli.py

@@ -555,12 +555,12 @@ class RecordCdsPubli(dict, AuthorsMixin, PublicationInfoMixin):
         else:
             self["prepublication"] = {"date": date}
 
-    def check_and_fix_record(self,
-                             db=None,
-                             fmt_author=None,
-                             rex_institute=None,
-                             sep_author=", ",
-                             sort_author=False):
+    def check_and_fix(self,
+                      db=None,
+                      fmt_author=None,
+                      rex_institute=None,
+                      sep_author=", ",
+                      sort_author=False):
         """Check record and fix non-conformities.
 
             * is with authors

modules/store_tools/recordheppubli.py

@@ -10,7 +10,7 @@ from .base import (search_synonym,
                    MSG_WELL_FORMED_DATE,
                    REG_DATE_YYYYMM,
                    T4, T6)
-from .exception import CheckException
+from .exception import CheckException, ToolException
 from filters import CLEAN_COLLABORATION
 from pandas import DataFrame
 from .publicationinfomixin import PublicationInfoMixin
@@ -237,13 +237,17 @@ class RecordHepPubli(dict, AuthorsMixin, PublicationInfoMixin):
         if len(val) == 0:
             return
 
-        dbid = search_synonym(db.collaborations, "collaboration", val)
-        if dbid == UNDEF_ID:
-            raise CheckException(MSG_UNKNOWN_COLLABORATION)
+        try:
+            dbid = search_synonym(db.collaborations, "collaboration", val)
+            if dbid == UNDEF_ID:
+                raise CheckException(MSG_UNKNOWN_COLLABORATION)
 
-        collaboration = db.collaborations[dbid].collaboration
-        if collaboration != val:
-            self["collaborations"] = [{"value": collaboration}]
+            collaboration = db.collaborations[dbid].collaboration
+            if collaboration != val:
+                self["collaborations"] = [{"value": collaboration}]
+
+        except ToolException as e:
+            raise CheckException(e)
 
     def check_my_affiliation(self, rex_institute=None):
         """Check that authors of my institute are signatories.
@@ -285,12 +289,12 @@ class RecordHepPubli(dict, AuthorsMixin, PublicationInfoMixin):
         if not REG_DATE_YYYYMM.match(xdate):
             raise CheckException(MSG_WELL_FORMED_DATE)
 
-    def check_and_fix_record(self,
-                             db=None,
-                             fmt_author=None,
-                             rex_institute=None,
-                             sep_author=", ",
-                             sort_author=False):
+    def check_and_fix(self,
+                      db=None,
+                      fmt_author=None,
+                      rex_institute=None,
+                      sep_author=", ",
+                      sort_author=False):
         """Check record and fix non-conformities.
 
             * is with authors