Removed incorrect HGVS validation and removed internal accessions from variant model.

Author: Alan Rubin

scoreset/models.py

@@ -390,7 +390,7 @@ class Meta:
     #                       Methods
     # ---------------------------------------------------------------------- #
     def __str__(self):
-        return str(self.accession)
+        return 'ID: {}, HGVS: {}'.format(str(self.pk), str(self.hgvs))
 
     @property
     def scores_columns(self):
@@ -413,18 +413,18 @@ def get_ordered_counts_data(self):
     def save(self, *args, **kwargs):
         with transaction.atomic():
             super(Variant, self).save(*args, **kwargs)
-            if not self.accession:
-                parent = self.scoreset
-                digit_suffix = parent.next_variant_suffix()
-                accession = '{}.{}'.format(
-                    parent.accession.replace(
-                        parent.ACCESSION_PREFIX, self.ACCESSION_PREFIX),
-                    digit_suffix
-                )
-                parent.last_used_suffix = digit_suffix
-                parent.save()
-                self.accession = accession
-                self.save()
+#            if not self.accession:
+#                parent = self.scoreset
+#                digit_suffix = parent.next_variant_suffix()
+#                accession = '{}.{}'.format(
+#                    parent.accession.replace(
+#                        parent.ACCESSION_PREFIX, self.ACCESSION_PREFIX),
+#                    digit_suffix
+#                )
+#                parent.last_used_suffix = digit_suffix
+#                parent.save()
+#                self.accession = accession
+#                self.save()
 
 
 @receiver(post_save, sender=ScoreSet)

scoreset/validators.py

@@ -58,20 +58,21 @@ def valid_var_accession(accession):
 
 
 def valid_hgvs_string(string):
-    variants = [v.strip() for v in string.strip().split(',')]
-
-    protein_matches = all([re_protein.match(v) for v in variants])
-    nucleotide_matches = all([re_nucleotide.match(v) for v in variants])
-    coding_matches = all([re_coding.match(v) for v in variants])
-    noncoding_matches = all([re_noncoding.match(v) for v in variants])
-    wt_or_sy = all([v in ["_wt", "_sy"] for v in variants])
-
-    if not (protein_matches or nucleotide_matches or
-            coding_matches or noncoding_matches or wt_or_sy):
-        raise ValidationError(
-            _("Variant '%(variant)s' is not a valid HGVS string."),
-            params={'variant': string}
-        )
+#    variants = [v.strip() for v in string.strip().split(',')]
+#
+#    protein_matches = all([re_protein.match(v) for v in variants])
+#    nucleotide_matches = all([re_nucleotide.match(v) for v in variants])
+#    coding_matches = all([re_coding.match(v) for v in variants])
+#    noncoding_matches = all([re_noncoding.match(v) for v in variants])
+#    wt_or_sy = all([v in ["_wt", "_sy"] for v in variants])
+#
+#    if not (protein_matches or nucleotide_matches or
+#            coding_matches or noncoding_matches or wt_or_sy):
+#        raise ValidationError(
+#            _("Variant '%(variant)s' is not a valid HGVS string."),
+#            params={'variant': string}
+#        )
+    return
 
 
 def valid_scoreset_score_data_input(file):