Adding fields to Hgnc.

HISTORY.rst

@@ -28,6 +28,7 @@ Full Change List
   It is currently not possible to migrate a GRCh37 case to GRCh38.
 - Setting ``VARFISH_CADD_SUBMISSION_RELEASE`` is called ``VARFISH_CADD_SUBMISSION_VERSION`` now (**breaking change**).
 - ``import_info.tsv`` expected as in data release from ``20210728`` as built from varfish-db-downloader ``1b03e97`` or later.
+- Extending  columns of ``Hgnc`` to upstream update.
 
 -------
 v0.23.9

geneinfo/migrations/0025_auto_20211019_0829.py

@@ -0,0 +1,22 @@
+# Generated by Django 3.2.7 on 2021-10-19 08:29
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("geneinfo", "0024_alter_ncbigenerif_pubmed_ids"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="hgnc", name="agr", field=models.CharField(max_length=32, null=True),
+        ),
+        migrations.AddField(
+            model_name="hgnc", name="lncipedia", field=models.CharField(max_length=32, null=True),
+        ),
+        migrations.AddField(
+            model_name="hgnc", name="mane_select", field=models.CharField(max_length=64, null=True),
+        ),
+    ]

geneinfo/migrations/0026_hgnc_gtrnadb.py

@@ -0,0 +1,16 @@
+# Generated by Django 3.2.7 on 2021-10-20 07:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("geneinfo", "0025_auto_20211019_0829"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="hgnc", name="gtrnadb", field=models.CharField(max_length=32, null=True),
+        ),
+    ]

geneinfo/models.py

@@ -107,6 +107,14 @@ class Hgnc(models.Model):
     intermediate_filament_db = models.CharField(max_length=32, null=True)
     #: RNACentral ID (rnacentral.org database)
     rna_central_ids = models.CharField(max_length=32, null=True)
+    #: gtrna DB ID
+    gtrnadb = models.CharField(max_length=32, null=True)
+    #: lcipedia.org IDs
+    lncipedia = models.CharField(max_length=32, null=True)
+    #: Alliance of genome resources.
+    agr = models.CharField(max_length=32, null=True)
+    #: MANE collected ID.
+    mane_select = models.CharField(max_length=64, null=True)
 
     #: Allow bulk import
     objects = CopyManager()

importer/management/commands/import_tables.py

@@ -302,6 +302,7 @@ def _handle_import(self, import_info, options):
                 TABLES[import_info["build"]][table_group],
                 force=options["force"],
                 truncate=options["truncate"],
+                release=import_info["build"],
             )
         # Special import routine for gene intervals
         elif table_group in ("ensembl_genes", "refseq_genes"):
@@ -549,6 +550,7 @@ def _import(
                     self.stderr.write(
                         "Error during import to table %s:\n%s" % (table._meta.db_table, e)
                     )
+                    traceback.print_exc(file=self.stderr)
                     # Remove already imported data.
                     sa_table = get_meta().tables[table._meta.db_table]
                     if "release" in sa_table.c:
@@ -639,9 +641,10 @@ def _replace_pk_in_kegg_and_import(self, mapping, path, release_info, table, for
     def _import_gnomad(self, path, tables, force, truncate):
         self._import_chromosome_wise(path, tables, force, truncate, list(range(1, 23)) + ["X"])
 
-    def _import_dbsnp(self, path, tables, force, truncate):
+    def _import_dbsnp(self, path, tables, force, truncate, release):
+        chr_mt = ["MT"] if release == "GRCh37" else ["M"]
         self._import_chromosome_wise(
-            path, tables, force, truncate, list(range(1, 23)) + ["X", "Y", "MT"]
+            path, tables, force, truncate, list(range(1, 23)) + ["X", "Y"] + chr_mt
         )
 
     def _import_chromosome_wise(self, path, tables, force, truncate, chroms):