diff --git a/vdw/samples/migrations/0036_in_dbsnp_nulls_to_false.py b/vdw/samples/migrations/0036_in_dbsnp_nulls_to_false.py new file mode 100644 index 0000000..9a58c44 --- /dev/null +++ b/vdw/samples/migrations/0036_in_dbsnp_nulls_to_false.py @@ -0,0 +1,299 @@ +# -*- coding: utf-8 -*- +import datetime +from south.db import db +from south.v2 import DataMigration +from django.db import models + +class Migration(DataMigration): + + def forwards(self, orm): + orm['samples.Result'].objects.filter(in_dbsnp__isnull=True)\ + .update(in_dbsnp=False) + + def backwards(self, orm): + # There is no safe way back because we are not sure what was null and + # what was already False when we moved forward. There should be no + # issue with leaving all the False values as False though and not + # having any nulls. + pass + + models = { + 'auth.group': { + 'Meta': {'object_name': 'Group'}, + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + 'auth.permission': { + 'Meta': {'ordering': "('content_type__app_label', 'content_type__model', 'codename')", 'unique_together': "(('content_type', 'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['contenttypes.ContentType']"}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + 'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Group']", 'symmetrical': 'False', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + 'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + 'genome.chromosome': { + 'Meta': {'ordering': "['order']", 'object_name': 'Chromosome', 'db_table': "'chromosome'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '2'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '2', 'db_index': 'True'}) + }, + 'genome.genome': { + 'Meta': {'object_name': 'Genome', 'db_table': "'genome'"}, + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'released': ('django.db.models.fields.DateField', [], {'null': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + 'genome.genotype': { + 'Meta': {'object_name': 'Genotype', 'db_table': "'genotype'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '3'}) + }, + 'literature.pubmed': { + 'Meta': {'object_name': 'PubMed', 'db_table': "'pubmed'"}, + 'pmid': ('django.db.models.fields.IntegerField', [], {'primary_key': 'True'}) + }, + 'phenotypes.phenotype': { + 'Meta': {'object_name': 'Phenotype', 'db_table': "'phenotype'"}, + 'articles': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['literature.PubMed']", 'symmetrical': 'False'}), + 'description': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'hpo_id': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'term': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '1000'}) + }, + 'samples.batch': { + 'Meta': {'ordering': "('project', 'label')", 'unique_together': "(('project', 'name'),)", 'object_name': 'Batch', 'db_table': "'batch'"}, + 'count': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'investigator': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'batches'", 'to': "orm['samples.Project']"}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}) + }, + 'samples.cohort': { + 'Meta': {'ordering': "('-order', 'name')", 'object_name': 'Cohort', 'db_table': "'cohort'"}, + 'allele_freq_modified': ('django.db.models.fields.DateTimeField', [], {'null': 'True'}), + 'autocreated': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'batch': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Batch']", 'null': 'True', 'blank': 'True'}), + 'count': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'order': ('django.db.models.fields.SmallIntegerField', [], {'default': '0'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Project']", 'null': 'True', 'blank': 'True'}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'samples': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Sample']", 'through': "orm['samples.CohortSample']", 'symmetrical': 'False'}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['auth.User']", 'null': 'True', 'blank': 'True'}) + }, + 'samples.cohortsample': { + 'Meta': {'object_name': 'CohortSample', 'db_table': "'cohort_sample'"}, + 'added': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'object_set': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Cohort']", 'db_column': "'cohort_id'"}), + 'removed': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'set_object': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Sample']", 'db_column': "'sample_id'"}) + }, + 'samples.cohortvariant': { + 'Meta': {'unique_together': "(('variant', 'cohort'),)", 'object_name': 'CohortVariant', 'db_table': "'cohort_variant'"}, + 'af': ('django.db.models.fields.FloatField', [], {'null': 'True', 'db_index': 'True'}), + 'cohort': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Cohort']"}), + 'id': ('vdw.core.models.BigAutoField', [], {'primary_key': 'True'}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'cohort_details'", 'to': "orm['variants.Variant']"}) + }, + 'samples.person': { + 'Meta': {'object_name': 'Person', 'db_table': "'person'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'mrn': ('django.db.models.fields.CharField', [], {'max_length': '50', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'proband': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'relations': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Person']", 'through': "orm['samples.Relation']", 'symmetrical': 'False'}), + 'sex': ('django.db.models.fields.CharField', [], {'max_length': '20', 'null': 'True', 'blank': 'True'}) + }, + 'samples.project': { + 'Meta': {'unique_together': "(('name',),)", 'object_name': 'Project', 'db_table': "'project'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}) + }, + 'samples.relation': { + 'Meta': {'ordering': "('person', '-generation')", 'object_name': 'Relation', 'db_table': "'relation'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'generation': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'person': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'family'", 'to': "orm['samples.Person']"}), + 'relative': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'relative_of'", 'to': "orm['samples.Person']"}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + }, + 'samples.result': { + 'Meta': {'unique_together': "(('sample', 'variant'),)", 'object_name': 'Result', 'db_table': "'sample_result'"}, + 'base_counts': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'baseq_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'coverage_alt': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'coverage_ref': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'downsampling': ('django.db.models.fields.NullBooleanField', [], {'null': 'True', 'blank': 'True'}), + 'fisher_strand': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'genotype': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Genotype']", 'null': 'True', 'blank': 'True'}), + 'genotype_quality': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'haplotype_score': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'homopolymer_run': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'id': ('vdw.core.models.BigAutoField', [], {'primary_key': 'True'}), + 'in_dbsnp': ('django.db.models.fields.NullBooleanField', [], {'null': 'True', 'blank': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'mq': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'mq0': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'mq_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'phred_scaled_likelihood': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'quality': ('django.db.models.fields.FloatField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'quality_by_depth': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'raw_read_depth': ('django.db.models.fields.IntegerField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'read_depth': ('django.db.models.fields.IntegerField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'read_pos_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'results'", 'to': "orm['samples.Sample']"}), + 'spanning_deletions': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'strand_bias': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['variants.Variant']"}) + }, + 'samples.resultscore': { + 'Meta': {'object_name': 'ResultScore', 'db_table': "'result_score'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'rank': ('django.db.models.fields.IntegerField', [], {}), + 'result': ('vdw.core.models.BigForeignKey', [], {'related_name': "'score'", 'unique': 'True', 'to': "orm['samples.Result']"}), + 'score': ('django.db.models.fields.FloatField', [], {}) + }, + 'samples.resultset': { + 'Meta': {'unique_together': "(('sample', 'name'),)", 'object_name': 'ResultSet', 'db_table': "'result_set'"}, + 'count': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'description': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'results': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Result']", 'through': "orm['samples.ResultSetItem']", 'symmetrical': 'False'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'result_sets'", 'to': "orm['samples.Sample']"}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['auth.User']"}) + }, + 'samples.resultsetitem': { + 'Meta': {'unique_together': "(('result', 'set'),)", 'object_name': 'ResultSetItem', 'db_table': "'result_set_item'"}, + 'added': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'removed': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Result']"}), + 'set': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.ResultSet']"}) + }, + 'samples.sample': { + 'Meta': {'ordering': "('project', 'batch', 'label')", 'unique_together': "(('batch', 'name', 'version'),)", 'object_name': 'Sample', 'db_table': "'sample'"}, + 'batch': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': "orm['samples.Batch']"}), + 'bio_sample': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'count': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'md5': ('django.db.models.fields.CharField', [], {'max_length': '32', 'null': 'True', 'blank': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'person': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'samples'", 'null': 'True', 'to': "orm['samples.Person']"}), + 'phenotype_modified': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': "orm['samples.Project']"}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'vcf_colname': ('django.db.models.fields.CharField', [], {'max_length': '200', 'null': 'True', 'blank': 'True'}), + 'version': ('django.db.models.fields.IntegerField', [], {}) + }, + 'samples.samplemanifest': { + 'Meta': {'object_name': 'SampleManifest', 'db_table': "'sample_manifest'"}, + 'content': ('django.db.models.fields.TextField', [], {}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'sample': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'manifest'", 'unique': 'True', 'to': "orm['samples.Sample']"}) + }, + 'samples.samplerun': { + 'Meta': {'object_name': 'SampleRun', 'db_table': "'sample_run'"}, + 'completed': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'genome': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Genome']", 'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Sample']"}) + }, + 'variants.variant': { + 'Meta': {'unique_together': "(('chr', 'pos', 'ref', 'alt'),)", 'object_name': 'Variant', 'db_table': "'variant'"}, + 'alt': ('django.db.models.fields.TextField', [], {'db_index': 'True'}), + 'articles': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['literature.PubMed']", 'db_table': "'variant_pubmed'", 'symmetrical': 'False'}), + 'chr': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Chromosome']"}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'liftover': ('django.db.models.fields.NullBooleanField', [], {'null': 'True', 'blank': 'True'}), + 'md5': ('django.db.models.fields.CharField', [], {'max_length': '32'}), + 'phenotypes': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['phenotypes.Phenotype']", 'through': "orm['variants.VariantPhenotype']", 'symmetrical': 'False'}), + 'pos': ('django.db.models.fields.IntegerField', [], {}), + 'ref': ('django.db.models.fields.TextField', [], {'db_index': 'True'}), + 'rsid': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'type': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['variants.VariantType']", 'null': 'True'}) + }, + 'variants.variantphenotype': { + 'Meta': {'object_name': 'VariantPhenotype', 'db_table': "'variant_phenotype'"}, + 'hgmd_id': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '30', 'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'phenotype': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['phenotypes.Phenotype']"}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'variant_phenotypes'", 'to': "orm['variants.Variant']"}) + }, + 'variants.varianttype': { + 'Meta': {'ordering': "['order']", 'object_name': 'VariantType', 'db_table': "'variant_type'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + } + } + + complete_apps = ['samples'] + symmetrical = True diff --git a/vdw/samples/migrations/0037_auto__chg_field_result_in_dbsnp__add_index_result_in_dbsnp.py b/vdw/samples/migrations/0037_auto__chg_field_result_in_dbsnp__add_index_result_in_dbsnp.py new file mode 100644 index 0000000..ef6f455 --- /dev/null +++ b/vdw/samples/migrations/0037_auto__chg_field_result_in_dbsnp__add_index_result_in_dbsnp.py @@ -0,0 +1,304 @@ +# -*- coding: utf-8 -*- +import datetime +from south.db import db +from south.v2 import SchemaMigration +from django.db import models + + +class Migration(SchemaMigration): + + def forwards(self, orm): + + # Changing field 'Result.in_dbsnp' + db.alter_column('sample_result', 'in_dbsnp', self.gf('django.db.models.fields.BooleanField')()) + # Adding index on 'Result', fields ['in_dbsnp'] + db.create_index('sample_result', ['in_dbsnp']) + + + def backwards(self, orm): + # Removing index on 'Result', fields ['in_dbsnp'] + db.delete_index('sample_result', ['in_dbsnp']) + + + # Changing field 'Result.in_dbsnp' + db.alter_column('sample_result', 'in_dbsnp', self.gf('django.db.models.fields.NullBooleanField')(null=True)) + + models = { + 'auth.group': { + 'Meta': {'object_name': 'Group'}, + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + 'auth.permission': { + 'Meta': {'ordering': "('content_type__app_label', 'content_type__model', 'codename')", 'unique_together': "(('content_type', 'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['contenttypes.ContentType']"}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + 'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Group']", 'symmetrical': 'False', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + 'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + 'genome.chromosome': { + 'Meta': {'ordering': "['order']", 'object_name': 'Chromosome', 'db_table': "'chromosome'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '2'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '2', 'db_index': 'True'}) + }, + 'genome.genome': { + 'Meta': {'object_name': 'Genome', 'db_table': "'genome'"}, + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'released': ('django.db.models.fields.DateField', [], {'null': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + 'genome.genotype': { + 'Meta': {'object_name': 'Genotype', 'db_table': "'genotype'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '3'}) + }, + 'literature.pubmed': { + 'Meta': {'object_name': 'PubMed', 'db_table': "'pubmed'"}, + 'pmid': ('django.db.models.fields.IntegerField', [], {'primary_key': 'True'}) + }, + 'phenotypes.phenotype': { + 'Meta': {'object_name': 'Phenotype', 'db_table': "'phenotype'"}, + 'articles': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['literature.PubMed']", 'symmetrical': 'False'}), + 'description': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'hpo_id': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'term': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '1000'}) + }, + 'samples.batch': { + 'Meta': {'ordering': "('project', 'label')", 'unique_together': "(('project', 'name'),)", 'object_name': 'Batch', 'db_table': "'batch'"}, + 'count': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'investigator': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'batches'", 'to': "orm['samples.Project']"}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}) + }, + 'samples.cohort': { + 'Meta': {'ordering': "('-order', 'name')", 'object_name': 'Cohort', 'db_table': "'cohort'"}, + 'allele_freq_modified': ('django.db.models.fields.DateTimeField', [], {'null': 'True'}), + 'autocreated': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'batch': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Batch']", 'null': 'True', 'blank': 'True'}), + 'count': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'order': ('django.db.models.fields.SmallIntegerField', [], {'default': '0'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Project']", 'null': 'True', 'blank': 'True'}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'samples': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Sample']", 'through': "orm['samples.CohortSample']", 'symmetrical': 'False'}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['auth.User']", 'null': 'True', 'blank': 'True'}) + }, + 'samples.cohortsample': { + 'Meta': {'object_name': 'CohortSample', 'db_table': "'cohort_sample'"}, + 'added': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'object_set': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Cohort']", 'db_column': "'cohort_id'"}), + 'removed': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'set_object': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Sample']", 'db_column': "'sample_id'"}) + }, + 'samples.cohortvariant': { + 'Meta': {'unique_together': "(('variant', 'cohort'),)", 'object_name': 'CohortVariant', 'db_table': "'cohort_variant'"}, + 'af': ('django.db.models.fields.FloatField', [], {'null': 'True', 'db_index': 'True'}), + 'cohort': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Cohort']"}), + 'id': ('vdw.core.models.BigAutoField', [], {'primary_key': 'True'}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'cohort_details'", 'to': "orm['variants.Variant']"}) + }, + 'samples.person': { + 'Meta': {'object_name': 'Person', 'db_table': "'person'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'mrn': ('django.db.models.fields.CharField', [], {'max_length': '50', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'proband': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'relations': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Person']", 'through': "orm['samples.Relation']", 'symmetrical': 'False'}), + 'sex': ('django.db.models.fields.CharField', [], {'max_length': '20', 'null': 'True', 'blank': 'True'}) + }, + 'samples.project': { + 'Meta': {'unique_together': "(('name',),)", 'object_name': 'Project', 'db_table': "'project'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}) + }, + 'samples.relation': { + 'Meta': {'ordering': "('person', '-generation')", 'object_name': 'Relation', 'db_table': "'relation'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'generation': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'person': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'family'", 'to': "orm['samples.Person']"}), + 'relative': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'relative_of'", 'to': "orm['samples.Person']"}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + }, + 'samples.result': { + 'Meta': {'unique_together': "(('sample', 'variant'),)", 'object_name': 'Result', 'db_table': "'sample_result'"}, + 'base_counts': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'baseq_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'coverage_alt': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'coverage_ref': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'downsampling': ('django.db.models.fields.NullBooleanField', [], {'null': 'True', 'blank': 'True'}), + 'fisher_strand': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'genotype': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Genotype']", 'null': 'True', 'blank': 'True'}), + 'genotype_quality': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'haplotype_score': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'homopolymer_run': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'id': ('vdw.core.models.BigAutoField', [], {'primary_key': 'True'}), + 'in_dbsnp': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'mq': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'mq0': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'mq_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'phred_scaled_likelihood': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'quality': ('django.db.models.fields.FloatField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'quality_by_depth': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'raw_read_depth': ('django.db.models.fields.IntegerField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'read_depth': ('django.db.models.fields.IntegerField', [], {'db_index': 'True', 'null': 'True', 'blank': 'True'}), + 'read_pos_rank_sum': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'results'", 'to': "orm['samples.Sample']"}), + 'spanning_deletions': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'strand_bias': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['variants.Variant']"}) + }, + 'samples.resultscore': { + 'Meta': {'object_name': 'ResultScore', 'db_table': "'result_score'"}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'rank': ('django.db.models.fields.IntegerField', [], {}), + 'result': ('vdw.core.models.BigForeignKey', [], {'related_name': "'score'", 'unique': 'True', 'to': "orm['samples.Result']"}), + 'score': ('django.db.models.fields.FloatField', [], {}) + }, + 'samples.resultset': { + 'Meta': {'unique_together': "(('sample', 'name'),)", 'object_name': 'ResultSet', 'db_table': "'result_set'"}, + 'count': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'description': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'results': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['samples.Result']", 'through': "orm['samples.ResultSetItem']", 'symmetrical': 'False'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'result_sets'", 'to': "orm['samples.Sample']"}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['auth.User']"}) + }, + 'samples.resultsetitem': { + 'Meta': {'unique_together': "(('result', 'set'),)", 'object_name': 'ResultSetItem', 'db_table': "'result_set_item'"}, + 'added': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'removed': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Result']"}), + 'set': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.ResultSet']"}) + }, + 'samples.sample': { + 'Meta': {'ordering': "('project', 'batch', 'label')", 'unique_together': "(('batch', 'name', 'version'),)", 'object_name': 'Sample', 'db_table': "'sample'"}, + 'batch': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': "orm['samples.Batch']"}), + 'bio_sample': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'count': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'md5': ('django.db.models.fields.CharField', [], {'max_length': '32', 'null': 'True', 'blank': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'person': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'samples'", 'null': 'True', 'to': "orm['samples.Person']"}), + 'phenotype_modified': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'project': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': "orm['samples.Project']"}), + 'published': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'vcf_colname': ('django.db.models.fields.CharField', [], {'max_length': '200', 'null': 'True', 'blank': 'True'}), + 'version': ('django.db.models.fields.IntegerField', [], {}) + }, + 'samples.samplemanifest': { + 'Meta': {'object_name': 'SampleManifest', 'db_table': "'sample_manifest'"}, + 'content': ('django.db.models.fields.TextField', [], {}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'sample': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'manifest'", 'unique': 'True', 'to': "orm['samples.Sample']"}) + }, + 'samples.samplerun': { + 'Meta': {'object_name': 'SampleRun', 'db_table': "'sample_run'"}, + 'completed': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'genome': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Genome']", 'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['samples.Sample']"}) + }, + 'variants.variant': { + 'Meta': {'unique_together': "(('chr', 'pos', 'ref', 'alt'),)", 'object_name': 'Variant', 'db_table': "'variant'"}, + 'alt': ('django.db.models.fields.TextField', [], {'db_index': 'True'}), + 'articles': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['literature.PubMed']", 'db_table': "'variant_pubmed'", 'symmetrical': 'False'}), + 'chr': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['genome.Chromosome']"}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'liftover': ('django.db.models.fields.NullBooleanField', [], {'null': 'True', 'blank': 'True'}), + 'md5': ('django.db.models.fields.CharField', [], {'max_length': '32'}), + 'phenotypes': ('django.db.models.fields.related.ManyToManyField', [], {'to': "orm['phenotypes.Phenotype']", 'through': "orm['variants.VariantPhenotype']", 'symmetrical': 'False'}), + 'pos': ('django.db.models.fields.IntegerField', [], {}), + 'ref': ('django.db.models.fields.TextField', [], {'db_index': 'True'}), + 'rsid': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'type': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['variants.VariantType']", 'null': 'True'}) + }, + 'variants.variantphenotype': { + 'Meta': {'object_name': 'VariantPhenotype', 'db_table': "'variant_phenotype'"}, + 'hgmd_id': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '30', 'null': 'True', 'blank': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'phenotype': ('django.db.models.fields.related.ForeignKey', [], {'to': "orm['phenotypes.Phenotype']"}), + 'variant': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'variant_phenotypes'", 'to': "orm['variants.Variant']"}) + }, + 'variants.varianttype': { + 'Meta': {'ordering': "['order']", 'object_name': 'VariantType', 'db_table': "'variant_type'"}, + 'code': ('django.db.models.fields.IntegerField', [], {'null': 'True'}), + 'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'label': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'order': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + } + } + + complete_apps = ['samples'] \ No newline at end of file diff --git a/vdw/samples/models.py b/vdw/samples/models.py index 3e3453d..e439730 100644 --- a/vdw/samples/models.py +++ b/vdw/samples/models.py @@ -338,7 +338,7 @@ class Result(TimestampedModel): phred_scaled_likelihood = models.TextField(null=True, blank=True) - in_dbsnp = models.NullBooleanField(blank=True) + in_dbsnp = models.BooleanField(default=False, db_index=True) downsampling = models.NullBooleanField(blank=True) spanning_deletions = models.FloatField(null=True, blank=True) mq = models.FloatField('mapping quality', null=True, blank=True) diff --git a/vdw/samples/pipeline/utils.py b/vdw/samples/pipeline/utils.py index 4fad4f1..21d7abe 100644 --- a/vdw/samples/pipeline/utils.py +++ b/vdw/samples/pipeline/utils.py @@ -53,6 +53,12 @@ def process_line(self, record): # Remove variant specific parts cleaned = cleaned[4:] + # in_dbsnp is not nullable so we need to replace null values with + # False for this line to be valid. in_dbsnp is the first column as + # determined by the `output_columns` defined above. + if cleaned[0] == '\\N': + cleaned[0] = False + # can these be indexed? call = record.genotype(self.vcf_sample)