Fix loading/retrieving date in BioSQL (see Bug 2681 and Cymon's analy…

…sis)

BioSQL/BioSeq.py

@@ -363,7 +363,8 @@ def _retrieve_qualifier_value(adaptor, primary_id):
     qualifiers = {}
     for name, value in qvs:
         if name == "keyword": name = "keywords"
-        elif name == "date_changed": name = "dates"
+        #See handling of "date" in Loader.py
+        elif name == "date_changed": name = "date"
         elif name == "secondary_accession": name = "accessions"
         qualifiers.setdefault(name, []).append(value)
     return qualifiers

BioSQL/Loader.py

@@ -653,7 +653,7 @@ def _load_annotations(self, record, bioentry_id):
                    " VALUES (%s, %s, %s, %s)"
         tag_ontology_id = self._get_ontology_id('Annotation Tags')
         for key, value in record.annotations.iteritems():
-            if key in ["references", "comment", "ncbi_taxid"]:
+            if key in ["references", "comment", "ncbi_taxid", "date"]:
                 #Handled separately
                 continue
             term_id = self._get_term_id(key, ontology_id=tag_ontology_id)

NEWS

@@ -19,10 +19,11 @@ Bio.SeqIO can now read and write IMGT files, a variant of the EMBL sequence
 text file format with longer feature indentation, and protein EMBL files
 (used in the EMBL patents database file epo_prt.dat).
 
-(At least) 7 people have contributed to this release, include 3 new people:
+(At least) 8 people have contributed to this release, include 3 new people:
 
 Bartek Wilczynski
 Bartosz Telenczuk (first contribution)
+Cymon Cox
 Eric Talevich
 Michiel de Hoon
 Peter Cock

Tests/seq_tests_common.py

@@ -267,7 +267,7 @@ def compare_record(old, new):
     #'ncbi_taxon' and 'gi'.
     #TODO - address these, see Bug 2681?
     new_keys = set(new.annotations).difference(old.annotations)
-    new_keys = new_keys.difference(['cross_references', 'dates', 
+    new_keys = new_keys.difference(['cross_references', 'date', 
                                     'data_file_division', 'ncbi_taxid', 'gi'])
     assert not new_keys, "Unexpected new annotation keys: %s" \
            % ", ".join(new_keys)

Tests/test_BioSQL.py

@@ -508,9 +508,6 @@ def loop(self, filename, format):
             for key in ["comment", "references", "db_source"]:
                 if key in old.annotations and key not in new.annotations:
                     del old.annotations[key]
-            #TODO - remove this hack one we write the date properly:
-            del old.annotations["date"]
-            del new.annotations["date"]
             self.assertTrue(compare_record(old, new))
         #Done
         server.close()