Merge branch '31-32-synonym' into 'master'

31 32  add synonym field to the table collaborations, coutries and publishers

* Modify the database schema.
* Add the script `mv_dbschema_0815` to modify the schema of existing databases.
* Add the new function `harvest_tools.search_synonym`.
* Add the methods `Automaton.search_collaboration`, `Automaton.search_country` and `Automaton.search_publisher`.
* Modify the `Msg` class and the harvester view to display the synonym when the record is rejected.
* Update the documentation.
* Add more tests.
* Close #5, #31, #32

See merge request !30

controllers/harvest.py

@@ -10,6 +10,7 @@ from harvest_tools import (build_harvester_tool,
                            DRY_RUN,
                            format_author_fr,
                            family_name_fr,
+                           search_synonym,
                            ToolException)
 from invenio_tools import (CheckAndFix,
                            CheckException,
@@ -145,8 +146,15 @@ def edit_insert():
         values['PublicationsAuthors_institute'] = record.my_authors
 
         # collaboration
-        recId = get_id(db.collaborations, collaboration=record.collaboration())
-        values['PublicationsId_collaborations'] = int(recId) if recId else UNDEF_ID
+        recId = UNDEF_ID
+        try:
+            recId = search_synonym(db.collaborations,
+                                   "collaboration",
+                                   record.collaboration())
+        except ToolException:
+            pass
+
+        values['PublicationsId_collaborations'] = int(recId)
 
         # teams, project, categories, origin
         values['PublicationsId_categories'] = int(selector.id_categories)
@@ -160,8 +168,15 @@ def edit_insert():
             check.clean_erratum(record)
             check.format_editor(record)
 
-            recId = get_id(db.publishers, abbreviation=record.paper_editor())
-            values['PublicationsId_publishers'] = int(recId) if recId else UNDEF_ID
+            recId = UNDEF_ID
+            try:
+                recId = search_synonym(db.publishers,
+                                       "abbreviation",
+                                       record.paper_editor())
+            except ToolException:
+                pass
+
+            values['PublicationsId_publishers'] = int(recId)
             values['PublicationsVolume'] = record.paper_volume()
             values['PublicationsPages'] = record.paper_pages()
 
@@ -181,10 +196,15 @@ def edit_insert():
                 values['PublicationsConference_dates'] = record.conference_dates()
                 values['PublicationsConference_town'] = record.conference_town()
 
-                recId = get_id(db.countries, country=record.conference_country())
-                values['PublicationsId_countries'] = \
-                recId if recId is not None else UNDEF_ID
+                recId = UNDEF_ID
+                try:
+                    recId = search_synonym(db.countries,
+                                           "country",
+                                           record.conference_country())
+                except ToolException:
+                    pass
 
+                values['PublicationsId_countries'] = int(recId)
                 values['PublicationsConference_speaker'] = record.first_author()
 
         # thesis

docs/api/conf.py

@@ -55,7 +55,7 @@ extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.viewcode']
 
 # autosummary configuration
-autosummary_generate = False
+autosummary_generate = True
 
 # intersphinx configuration
 intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None)}

docs/api/generated/automaton/harvest_tools.automaton.Automaton.__init__.rst

-harvest_tools.automaton.Automaton.__init__
-==========================================
-
-.. currentmodule:: harvest_tools.automaton
-
-.. automethod:: Automaton.__init__
\ No newline at end of file

docs/api/generated/automaton/harvest_tools.automaton.Automaton.get_create_collaboration.rst

-harvest_tools.automaton.Automaton.get_create_collaboration
-==========================================================
-
-.. currentmodule:: harvest_tools.automaton
-
-.. automethod:: Automaton.get_create_collaboration
\ No newline at end of file

docs/api/generated/automaton/harvest_tools.automaton.Automaton.get_create_publisher.rst → docs/api/generated/automaton/harvest_tools.automaton.Automaton.search_collaboration.rst

-harvest_tools.automaton.Automaton.get_create_publisher
+harvest_tools.automaton.Automaton.search_collaboration
 ======================================================
 
 .. currentmodule:: harvest_tools.automaton
 
-.. automethod:: Automaton.get_create_publisher
\ No newline at end of file
+.. automethod:: Automaton.search_collaboration
\ No newline at end of file

docs/api/generated/automaton/harvest_tools.automaton.Automaton.search_country.rst

+harvest_tools.automaton.Automaton.search_country
+================================================
+
+.. currentmodule:: harvest_tools.automaton
+
+.. automethod:: Automaton.search_country
\ No newline at end of file

docs/api/generated/automaton/harvest_tools.automaton.Automaton.search_publisher.rst

+harvest_tools.automaton.Automaton.search_publisher
+==================================================
+
+.. currentmodule:: harvest_tools.automaton
+
+.. automethod:: Automaton.search_publisher
\ No newline at end of file

docs/api/generated/harvest_tools.articles.Articles.rst

@@ -12,15 +12,9 @@ harvest_tools.articles.Articles
       :toctree: articles/
 
       ~Articles.check_record
-      ~Articles.decode_xml
-      ~Articles.get_create_collaboration
-      ~Articles.get_create_publisher
       ~Articles.get_record_by_fields
       ~Articles.get_record_by_origin
       ~Articles.insert_record
-      ~Articles.process_url
-      ~Articles.process_xml
-      ~Articles.report
 
 
 

docs/api/generated/harvest_tools.automaton.Automaton.rst

@@ -4,23 +4,22 @@ harvest_tools.automaton.Automaton
 .. currentmodule:: harvest_tools.automaton
 
 .. autoclass:: Automaton
-   :show-inheritance:
 
    .. rubric:: Methods
 
    .. autosummary::
       :toctree: automaton/
 
-      ~Automaton.__init__
       ~Automaton.check_record
       ~Automaton.decode_xml
-      ~Automaton.get_create_collaboration
-      ~Automaton.get_create_publisher
       ~Automaton.get_record_by_fields
       ~Automaton.insert_record
       ~Automaton.process_url
       ~Automaton.process_xml
       ~Automaton.report
+      ~Automaton.search_collaboration
+      ~Automaton.search_country
+      ~Automaton.search_publisher
 
 
 

docs/api/generated/harvest_tools.automaton.search_synonym.rst

+harvest_tools.automaton.search_synonym
+======================================
+
+.. currentmodule:: harvest_tools.automaton
+
+.. autofunction:: search_synonym
\ No newline at end of file

docs/api/generated/harvest_tools.base.search_synonym.rst

+harvest_tools.base.search_synonym
+=================================
+
+.. currentmodule:: harvest_tools.base
+
+.. autofunction:: search_synonym
\ No newline at end of file

docs/api/generated/harvest_tools.notes.Notes.rst

@@ -12,14 +12,7 @@ harvest_tools.notes.Notes
       :toctree: notes/
 
       ~Notes.check_record
-      ~Notes.decode_xml
-      ~Notes.get_create_collaboration
-      ~Notes.get_create_publisher
-      ~Notes.get_record_by_fields
       ~Notes.insert_record
-      ~Notes.process_url
-      ~Notes.process_xml
-      ~Notes.report
 
 
 

docs/api/generated/harvest_tools.preprints.Preprints.rst

@@ -12,14 +12,7 @@ harvest_tools.preprints.Preprints
       :toctree: preprints/
 
       ~Preprints.check_record
-      ~Preprints.decode_xml
-      ~Preprints.get_create_collaboration
-      ~Preprints.get_create_publisher
-      ~Preprints.get_record_by_fields
       ~Preprints.insert_record
-      ~Preprints.process_url
-      ~Preprints.process_xml
-      ~Preprints.report
 
 
 

docs/api/generated/harvest_tools.proceedings.Proceedings.rst

@@ -12,14 +12,7 @@ harvest_tools.proceedings.Proceedings
       :toctree: proceedings/
 
       ~Proceedings.check_record
-      ~Proceedings.decode_xml
-      ~Proceedings.get_create_collaboration
-      ~Proceedings.get_create_publisher
-      ~Proceedings.get_record_by_fields
       ~Proceedings.insert_record
-      ~Proceedings.process_url
-      ~Proceedings.process_xml
-      ~Proceedings.report
 
 
 

docs/api/generated/harvest_tools.reports.Reports.rst

@@ -12,14 +12,7 @@ harvest_tools.reports.Reports
       :toctree: reports/
 
       ~Reports.check_record
-      ~Reports.decode_xml
-      ~Reports.get_create_collaboration
-      ~Reports.get_create_publisher
-      ~Reports.get_record_by_fields
       ~Reports.insert_record
-      ~Reports.process_url
-      ~Reports.process_xml
-      ~Reports.report
 
 
 

docs/api/generated/harvest_tools.talks.Talks.rst

@@ -12,14 +12,7 @@ harvest_tools.talks.Talks
       :toctree: talks/
 
       ~Talks.check_record
-      ~Talks.decode_xml
-      ~Talks.get_create_collaboration
-      ~Talks.get_create_publisher
-      ~Talks.get_record_by_fields
       ~Talks.insert_record
-      ~Talks.process_url
-      ~Talks.process_xml
-      ~Talks.report
 
 
 

docs/api/generated/harvest_tools.thesis.Thesis.rst

@@ -12,14 +12,7 @@ harvest_tools.thesis.Thesis
       :toctree: thesis/
 
       ~Thesis.check_record
-      ~Thesis.decode_xml
-      ~Thesis.get_create_collaboration
-      ~Thesis.get_create_publisher
-      ~Thesis.get_record_by_fields
       ~Thesis.insert_record
-      ~Thesis.process_url
-      ~Thesis.process_xml
-      ~Thesis.report
 
 
 

docs/api/generated/invenio_tools.checkandfix.CheckAndFix.rst

@@ -4,7 +4,6 @@ invenio_tools.checkandfix.CheckAndFix
 .. currentmodule:: invenio_tools.checkandfix
 
 .. autoclass:: CheckAndFix
-   :show-inheritance:
 
    .. rubric:: Methods
 

docs/api/generated/invenio_tools.inveniostore.InvenioStore.rst

@@ -4,7 +4,6 @@ invenio_tools.inveniostore.InvenioStore
 .. currentmodule:: invenio_tools.inveniostore
 
 .. autoclass:: InvenioStore
-   :show-inheritance:
 
    .. rubric:: Methods
 

docs/api/generated/invenio_tools.iterrecord.IterRecord.rst

@@ -4,7 +4,6 @@ invenio_tools.iterrecord.IterRecord
 .. currentmodule:: invenio_tools.iterrecord
 
 .. autoclass:: IterRecord
-   :show-inheritance:
 
    .. rubric:: Methods