class Migration(migrations.Migration):
dependencies = [
("projectroles", "0013_update_appsetting_type"),
("bgjobs", "0005_auto_20190128_1210"),
("variants", "0071_smallvariantflags_flag_molecular"),
]
operations = [
migrations.CreateModel(
name="DeleteCaseBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Job UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="variants_deletecasebgjob_related",
to="bgjobs.BackgroundJob",
),
),
(
"case",
models.ForeignKey(
help_text="The case to delete",
on_delete=django.db.models.deletion.CASCADE,
to="variants.Case",
),
),
(
"project",
models.ForeignKey(
help_text="Project in which this object belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
]
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
("bgjobs", "0005_auto_20190128_1210"),
("projectroles", "0006_add_remote_projects"),
("variants", "0029_auto_20190306_0727"),
]
operations = [
migrations.CreateModel(
name="ClinvarBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text=
"Background job for clinvar filtering and storing query results",
on_delete=django.db.models.deletion.CASCADE,
related_name="clinvar_bg_job",
to="bgjobs.BackgroundJob",
),
),
(
"case",
models.ForeignKey(
help_text="The case to filter",
on_delete=django.db.models.deletion.CASCADE,
to="variants.Case",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="ClinvarQuery",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(
default=uuid.uuid4,
help_text="Small variant flags SODAR UUID",
unique=True),
),
("form_id",
models.CharField(help_text="Identifier of the form",
max_length=100)),
("form_version",
models.IntegerField(help_text="Version of form when saving")),
(
"query_settings",
django.contrib.postgres.fields.jsonb.JSONField(
help_text="The query settings"),
),
(
"name",
models.CharField(
default=None,
help_text="Optional user-assigned name",
max_length=100,
null=True,
),
),
(
"public",
models.BooleanField(
default=False,
help_text="Case is flagged as public or not"),
),
(
"case",
models.ForeignKey(
help_text="The case that the query relates to",
on_delete=django.db.models.deletion.CASCADE,
related_name="clinvar_queries",
to="variants.Case",
),
),
("query_results",
models.ManyToManyField(to="variants.SmallVariant")),
(
"user",
models.ForeignKey(
blank=True,
help_text="User who created the query",
null=True,
on_delete=django.db.models.deletion.SET_NULL,
related_name="variants_clinvarquery_related",
to=settings.AUTH_USER_MODEL,
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False
},
),
migrations.AlterField(
model_name="projectcasessmallvariantquery",
name="project",
field=models.ForeignKey(
help_text="The project that the query relates to",
on_delete=django.db.models.deletion.CASCADE,
related_name="small_variant_queries",
to="variants.CaseAwareProject",
),
),
migrations.AddField(
model_name="clinvarbgjob",
name="clinvarquery",
field=models.ForeignKey(
help_text="Query that is executed.",
on_delete=django.db.models.deletion.CASCADE,
to="variants.ClinvarQuery",
),
),
migrations.AddField(
model_name="clinvarbgjob",
name="project",
field=models.ForeignKey(
help_text="Project in which this objects belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
]
class Migration(migrations.Migration):
dependencies = [
("projectroles", "0015_fix_appsetting_constraint"),
("bgjobs", "0006_auto_20200526_1657"),
("variants", "0079_auto_20210204_1006"),
]
operations = [
migrations.CreateModel(
name="SpanrSubmissionBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"query_args",
django.contrib.postgres.fields.jsonb.JSONField(
help_text="(Validated) query parameters"),
),
(
"spanr_job_url",
models.CharField(help_text="The SPANR job URL",
max_length=100,
null=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="spanr_submission_bg_job",
to="bgjobs.BackgroundJob",
),
),
(
"case",
models.ForeignKey(
help_text="The case to export",
on_delete=django.db.models.deletion.CASCADE,
to="variants.Case",
),
),
(
"project",
models.ForeignKey(
help_text="Project in which this objects belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
]
class Migration(migrations.Migration):
dependencies = [
("bgjobs", "0005_auto_20190128_1210"),
("projectroles", "0010_update_appsetting"),
("variants", "0047_auto_20190701_1625"),
]
operations = [
migrations.CreateModel(
name="ImportVariantsBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Job UUID",
unique=True),
),
("case_name",
models.CharField(help_text="The case name", max_length=128)),
("index_name",
models.CharField(help_text="The index name", max_length=128)),
("path_ped",
models.CharField(help_text="Path to PED file",
max_length=4096)),
(
"path_genotypes",
django.contrib.postgres.fields.ArrayField(
base_field=models.CharField(
help_text="Path to variants TSV file",
max_length=4096),
size=None,
),
),
(
"path_db_info",
django.contrib.postgres.fields.ArrayField(
base_field=models.CharField(
help_text="Path to db-info TSV file",
max_length=4096),
size=None,
),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="variants_importvariantsbgjob_related",
to="bgjobs.BackgroundJob",
),
),
(
"project",
models.ForeignKey(
help_text="Project that is imported to",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
)
]
class Migration(migrations.Migration):
dependencies = [
("projectroles", "0015_fix_appsetting_constraint"),
("bgjobs", "0006_auto_20200526_1657"),
(
"variants",
"0073_clearexpiredexportedfilesbgjob_clearinactivevariantsetsbgjob_clearoldkioskcasesbgjob_refreshsmallvar",
),
]
operations = [
migrations.CreateModel(
name="CaddSubmissionBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"query_args",
django.contrib.postgres.fields.jsonb.JSONField(
help_text="(Validated) query parameters"),
),
(
"cadd_version",
models.CharField(
help_text="The CADD version used for the annotation",
max_length=100),
),
(
"cadd_job_id",
models.CharField(
help_text=
"The project ID that CADD assigned on submission",
max_length=100,
null=True,
),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="cadd_submission_bg_job",
to="bgjobs.BackgroundJob",
),
),
(
"case",
models.ForeignKey(
help_text="The case to export",
on_delete=django.db.models.deletion.CASCADE,
to="variants.Case",
),
),
(
"project",
models.ForeignKey(
help_text="Project in which this objects belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
]
class Migration(migrations.Migration):
dependencies = [
("projectroles", "0006_add_remote_projects"),
("bgjobs", "0004_backgroundjob_user"),
("variants", "0019_rebuild_var_stats"),
]
operations = [
migrations.CreateModel(
name="ComputeProjectVariantsStatsBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Job Specialization SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="compute_project_variants_stats",
to="bgjobs.BackgroundJob",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="ProjectRelatedness",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
("sample1", models.CharField(max_length=200)),
("sample2", models.CharField(max_length=200)),
("het_1_2", models.IntegerField()),
("het_1", models.IntegerField()),
("het_2", models.IntegerField()),
("n_ibs0", models.IntegerField()),
("n_ibs1", models.IntegerField()),
("n_ibs2", models.IntegerField()),
],
options={
"ordering": ("sample1", "sample2"),
"abstract": False
},
),
migrations.CreateModel(
name="ProjectVariantStats",
fields=[(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
)],
),
migrations.CreateModel(
name="CaseAwareProject",
fields=[],
options={
"proxy": True,
"indexes": []
},
bases=("projectroles.project", ),
),
migrations.AlterField(
model_name="pedigreerelatedness",
name="stats",
field=models.ForeignKey(
help_text="Pedigree relatedness information",
on_delete=django.db.models.deletion.CASCADE,
related_name="relatedness",
to="variants.CaseVariantStats",
),
),
migrations.AddField(
model_name="projectvariantstats",
name="project",
field=models.OneToOneField(
help_text="The variant statistics object for this projects",
on_delete=django.db.models.deletion.CASCADE,
related_name="variant_stats",
to="projectroles.Project",
),
),
migrations.AddField(
model_name="projectrelatedness",
name="stats",
field=models.ForeignKey(
help_text="Pedigree relatedness information",
on_delete=django.db.models.deletion.CASCADE,
related_name="relatedness",
to="variants.ProjectVariantStats",
),
),
migrations.AddField(
model_name="computeprojectvariantsstatsbgjob",
name="project",
field=models.ForeignKey(
help_text="Project in which this objects belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
]
class Migration(migrations.Migration):
dependencies = [
("projectroles", "0009_rename_projectsetting"),
("bgjobs", "0005_auto_20190128_1210"),
("variants", "0042_auto_20190619_1636"),
]
operations = [
migrations.CreateModel(
name="SyncCaseListBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Job UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="variants_synccaselistbgjob_related",
to="bgjobs.BackgroundJob",
),
),
(
"project",
models.ForeignKey(
help_text="Project that is to be synced",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="SyncCaseResultMessage",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Message UUID",
unique=True),
),
(
"level",
models.CharField(
choices=[
("debug", "debug"),
("info", "info"),
("warning", "warning"),
("error", "error"),
],
help_text="Level of log entry",
max_length=50,
),
),
("message", models.TextField(help_text="Log level's message")),
(
"project",
models.ForeignKey(
help_text="Project for the message",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
),
]
class Migration(migrations.Migration):
dependencies = [
("projectroles", "0006_add_remote_projects"),
("bgjobs", "0004_backgroundjob_user"),
("variants", "0021_auto_20181127_0911"),
]
operations = [
migrations.CreateModel(
name="ExportProjectCasesFileBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"query_args",
django.contrib.postgres.fields.jsonb.JSONField(
help_text="(Validated) query parameters"),
),
(
"file_type",
models.CharField(
choices=[
("tsv", "TSV File"),
("xlsx", "Excel File (XLSX)"),
("vcf", "VCF File"),
],
help_text="File types for exported file",
max_length=32,
),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name=
"variants_exportprojectcasesfilebgjob_related",
to="bgjobs.BackgroundJob",
),
),
(
"project",
models.ForeignKey(
help_text="Project in which this objects belongs",
on_delete=django.db.models.deletion.CASCADE,
to="projectroles.Project",
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False
},
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="ExportProjectCasesFileBgJobResult",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"expiry_time",
models.DateTimeField(
help_text="Time at which the file download expires"),
),
("payload",
models.BinaryField(help_text="Resulting exported file")),
(
"job",
models.OneToOneField(
help_text="Related file export job",
on_delete=django.db.models.deletion.CASCADE,
related_name="export_result",
to="variants.ExportProjectCasesFileBgJob",
),
),
],
),
migrations.AlterModelOptions(name="exportfilebgjob",
options={"ordering":
("-date_created", )}),
migrations.AddField(
model_name="exportfilebgjob",
name="date_created",
field=models.DateTimeField(
auto_now_add=True,
default=django.utils.timezone.now,
help_text="DateTime of creation",
),
preserve_default=False,
),
migrations.AlterField(
model_name="exportfilebgjob",
name="bg_job",
field=models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="variants_exportfilebgjob_related",
to="bgjobs.BackgroundJob",
),
),
migrations.AlterField(
model_name="exportfilebgjob",
name="file_type",
field=models.CharField(
choices=[("tsv", "TSV File"), ("xlsx", "Excel File (XLSX)"),
("vcf", "VCF File")],
help_text="File types for exported file",
max_length=32,
),
),
]
class Migration(migrations.Migration):
dependencies = [
("bgjobs", "0006_auto_20200526_1657"),
("variants", "0072_deletecasebgjob"),
]
operations = [
migrations.CreateModel(
name="ClearExpiredExportedFilesBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name=
"variants_clearexpiredexportedfilesbgjob_related",
to="bgjobs.BackgroundJob",
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False,
},
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="ClearInactiveVariantSetsBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name=
"variants_clearinactivevariantsetsbgjob_related",
to="bgjobs.BackgroundJob",
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False,
},
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="ClearOldKioskCasesBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name="variants_clearoldkioskcasesbgjob_related",
to="bgjobs.BackgroundJob",
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False,
},
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
migrations.CreateModel(
name="RefreshSmallVariantSummaryBgJob",
fields=[
(
"id",
models.AutoField(auto_created=True,
primary_key=True,
serialize=False,
verbose_name="ID"),
),
(
"date_created",
models.DateTimeField(auto_now_add=True,
help_text="DateTime of creation"),
),
(
"sodar_uuid",
models.UUIDField(default=uuid.uuid4,
help_text="Case SODAR UUID",
unique=True),
),
(
"bg_job",
models.ForeignKey(
help_text="Background job for state etc.",
on_delete=django.db.models.deletion.CASCADE,
related_name=
"variants_refreshsmallvariantsummarybgjob_related",
to="bgjobs.BackgroundJob",
),
),
],
options={
"ordering": ("-date_created", ),
"abstract": False,
},
bases=(bgjobs.models.JobModelMessageMixin, models.Model),
),
]