Merge 3ae12b5 into 2e34f88

HISTORY.rst

@@ -2,9 +2,9 @@
 History / Changelog
 ===================
 
------------------
-HEAD (unreleased)
------------------
+-------
+v0.23.0
+-------
 
 End-User Summary
 ================
@@ -30,6 +30,8 @@ End-User Summary
 - Rebuild of variant summary database table happens every Sunday at 2:22am.
 - Added celery queues ``maintenance`` and ``export``.
 - Adding support for connecting two sites via the GAGH Beacon protocol.
+- Adding link-out to "GenCC".
+- Adding "submit to SPANR" feature.
 
 Full Change List
 ================
@@ -58,6 +60,8 @@ Full Change List
 - Added celery queues ``maintenance`` and ``export``.
 - Adding support for connecting two sites via the GAGH Beacon protocol.
 - Making CADD version behind CADD REST API configurable.
+- Adding link-out to "GenCC".
+- Adding "submit to SPANR" feature.
 
 -------
 v0.22.1

Makefile

@@ -5,6 +5,10 @@ MANAGE = time python manage.py
 black:
 	black -l 100 --exclude '/(\.eggs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.?v?env|_build|buck-out|build|dist|src)/' $(arg) .
 
+.PHONY: npm-install
+npm-install:
+	cd varfish/vueapp && npm ci
+
 .PHONY: serve
 serve:
 	$(MANAGE) runserver

README.rst

@@ -70,5 +70,5 @@ VarFish Data Release Compatibility Table
 =====================  ============  ==============
 VarFish DB Downloader  Data Release  VarFish Server
 =====================  ============  ==============
-v0.2                   20201006      <= v0.22.1
+v0.2                   20201006      <= v0.23
 =====================  ============  ==============

config/settings/base.py

@@ -487,6 +487,9 @@ def fixed_array_type(field):
 VARFISH_MUTATIONTASTER_BATCH_VARS = env.int("VARFISH_MUTATIONTASTER_BATCH_VARS", 50)
 VARFISH_MUTATIONTASTER_MAX_VARS = env.int("VARFISH_MUTATIONTASTER_MAX_VARS", 500)
 
+# VarfFish: Enable SPANR
+VARFISH_ENABLE_SPANR_SUBMISSION = env.bool("VARFISH_ENABLE_SPANR_SUBMISSION", False)
+
 # Varfish: UMD URL
 VARFISH_UMD_REST_API_URL = env.str(
     "VARFISH_UMD_REST_API_URL", "http://umd-predictor.eu/webservice.php"

docs_manual/admin_upgrade.rst

@@ -6,20 +6,16 @@ Upgrade Varfish Installation
 
 This section contains upgrade instructions for upgrading your VarFish Server installation using `VarFish Docker Compose <https://github.com/bihealth/varfish-docker-compose>`__.
 
--------------------------------------
-v0.22.1 to v0.23.0 (work in progress)
--------------------------------------
-
-.. warning::
-
-    Version v0.23.0 has not been released yet.
-    We can only provide support once v0.23.0 has been officially released.
+------------------
+v0.22.1 to v0.23.0
+------------------
 
 **Summary**
 
 - The Docker Compose installer now provides support for setting up CADD score annotation via `cadd-rest-api <https://github.com/bihealth/cadd-rest-api>`__.
-- The environment variable ``FIELD_ENCRYPTION_KEY`` **should** be setup properly.
+- The environment variable ``FIELD_ENCRYPTION_KEY`` **should** be setup properly by the user.
 - Two new celery queues are needed: ``maintenance`` and ``export``.
+- To enable the new and optional feature for uploading variants to SPANR you have to set the environment variable ``VARFISH_ENABLE_SPANR_SUBMISSION`` to ``1``.
 
 Detailed Instructions
 =====================

docs_manual/variants_filtration.rst

@@ -324,6 +324,13 @@ Here are the actions to create the recommended settings for submitting to Mutati
     The MutationDistiller submission uses the same feature as th VarFish VCF export.
     Thus, the limitations described in :ref:`download-as-file` apply.
 
+Submit to SPANR
+---------------
+
+Also, the little triangle next to the :guilabel:`Filter & Display` gives you access to the :guilabel:`Submit to SPANR` action.
+This is similar to submitting ot MutationDistiller described above.
+Clicking the button will submit the data to SPANR after confirming this once again in popup window.
+
 --------------------------
 Variant Filtration Results
 --------------------------

variants/admin.py

@@ -16,6 +16,7 @@
     SyncCaseResultMessage,
     ImportVariantsBgJob,
     SmallVariantSet,
+    SpanrSubmissionBgJob,
     CasePhenotypeTerms,
 )
 
@@ -37,6 +38,7 @@
         SyncCaseResultMessage,
         ImportVariantsBgJob,
         SmallVariantSet,
+        SpanrSubmissionBgJob,
         CasePhenotypeTerms,
     )
 )

variants/file_export.py

@@ -437,6 +437,7 @@ def write_tmp_file(self):
         self._write_variants()
         self._write_trailing()
         #: Rewind temporary file to beginning and return it.
+        self.tmp_file.flush()
         self.tmp_file.seek(0)
         return self.tmp_file
 

variants/forms.py

@@ -1375,6 +1375,7 @@ class FilterForm(
             ("download", "Generate downloadable file in background"),
             ("submit-mutationdistiller", "Submit to MutationDistiller"),
             ("submit-cadd", "Submit to CADD"),
+            ("submit-spanr", "Submit to SPANR"),
         )
     )
 

variants/migrations/0080_spanrsubmissionbgjob.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2021-04-01 08:45
+from __future__ import unicode_literals
+import uuid
+
+import bgjobs.models
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+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),
+        ),
+    ]

variants/models.py

@@ -612,6 +612,7 @@ def get_background_jobs(self):
             Q(variants_exportfilebgjob_related__case=self)
             | Q(cadd_submission_bg_job__case=self)
             | Q(distiller_submission_bg_job__case=self)
+            | Q(spanr_submission_bg_job__case=self)
             | Q(filter_bg_job__case=self)
         )
 
@@ -1228,6 +1229,43 @@ def get_absolute_url(self):
         )
 
 
+class SpanrSubmissionBgJob(JobModelMessageMixin, models.Model):
+    """Background job for submitting variants to SPANR."""
+
+    #: Task description for logging.
+    task_desc = "Submission to SPANR"
+
+    #: String identifying model in BackgroundJob.
+    spec_name = "variants.spanr_submission_bg_job"
+
+    # Fields required by SODAR
+    sodar_uuid = models.UUIDField(
+        default=uuid_object.uuid4, unique=True, help_text="Case SODAR UUID"
+    )
+    project = models.ForeignKey(Project, help_text="Project in which this objects belongs")
+
+    bg_job = models.ForeignKey(
+        BackgroundJob,
+        null=False,
+        related_name="spanr_submission_bg_job",
+        help_text="Background job for state etc.",
+        on_delete=models.CASCADE,
+    )
+    case = models.ForeignKey(Case, null=False, help_text="The case to export")
+    query_args = JSONField(null=False, help_text="(Validated) query parameters")
+
+    spanr_job_url = models.CharField(max_length=100, null=True, help_text="The SPANR job URL")
+
+    def get_human_readable_type(self):
+        return "SPANR Submission"
+
+    def get_absolute_url(self):
+        return reverse(
+            "variants:spanr-job-detail",
+            kwargs={"project": self.project.sodar_uuid, "job": self.sodar_uuid},
+        )
+
+
 class SmallVariantComment(models.Model):
     """Model for commenting on a ``SmallVariant``."""
 

variants/plugins.py

@@ -12,6 +12,7 @@
     ExportFileBgJob,
     ExportProjectCasesFileBgJob,
     CaddSubmissionBgJob,
+    SpanrSubmissionBgJob,
     DistillerSubmissionBgJob,
     ComputeProjectVariantsStatsBgJob,
     FilterBgJob,
@@ -280,6 +281,7 @@ class BackgroundJobsPlugin(BackgroundJobsPluginPoint):
     job_specs = {
         ExportFileBgJob.spec_name: ExportFileBgJob,
         CaddSubmissionBgJob.spec_name: CaddSubmissionBgJob,
+        SpanrSubmissionBgJob.spec_name: SpanrSubmissionBgJob,
         DistillerSubmissionBgJob.spec_name: DistillerSubmissionBgJob,
         ComputeProjectVariantsStatsBgJob.spec_name: ComputeProjectVariantsStatsBgJob,
         ExportProjectCasesFileBgJob.spec_name: ExportProjectCasesFileBgJob,

variants/queries.py

@@ -223,6 +223,8 @@ def __init__(self, *args, **kwargs):
                     func.max(Hgnc.sa.gene_family).label("gene_family"),
                     func.max(Hgnc.sa.pubmed_id).label("pubmed_id"),
                     func.max(Hgnc.sa.ucsc_id_novers).label("ucsc_id_novers"),
+                    func.max(Hgnc.sa.hgnc_id).label("hgnc_id"),
+                    func.max(Hgnc.sa.uniprot_ids).label("uniprot_ids"),
                 ]
             )
             .select_from(Hgnc.sa)
@@ -242,6 +244,8 @@ def extend_fields(self, _query_parts):
             func.coalesce(self.subquery_hgnc.c.name, "").label("gene_name"),
             func.coalesce(self.subquery_hgnc.c.gene_family, "").label("gene_family"),
             func.coalesce(self.subquery_hgnc.c.pubmed_id, "").label("pubmed_id"),
+            func.coalesce(self.subquery_hgnc.c.hgnc_id, "").label("hgnc_id"),
+            func.coalesce(self.subquery_hgnc.c.uniprot_ids, "").label("uniprot_ids"),
         ]