Merge 157654f into 591d9f8

HISTORY.rst

@@ -6,6 +6,8 @@ History / Changelog
 HEAD (unreleased)
 -----------------
 
+Breaking changes, see below.
+
 End-User Summary
 ================
 
@@ -25,6 +27,10 @@ End-User Summary
 - Added section for developers in manual (#267).
 - Migrated icons to iconify (#208).
 - Bumped chrome-driver version (#208).
+- VarFish now allows for the import of GRCh38 annotated variants.
+  For this, GRCh38 background data must be imported.
+  Kiosk mode does not support GRCh38 yet.
+  **This is a breaking change, new data and CLI must be used!**
 
 Full Change List
 ================
@@ -50,6 +56,13 @@ Full Change List
 - Migrated icons to iconify (#208).
 - Bumped chrome-driver version (#208).
 - Skipping codacy if token is not defined (#275).
+- Adjusting models and UI for supporting GRCh38 annotated cases.
+  It is currently not possible to migrate a GRCh37 case to GRCh38.
+- Adjusting models and UI for supporting GRCh38 annotated cases.
+  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

cohorts/templates/cohorts/cohort_create.html

@@ -112,6 +112,7 @@ <h5 class="mb-0">
           '    <span class="badge-group">' +
           '      <span class="badge badge-secondary">{{ label }}</span>' +
           '      <span class="badge badge-info members-count">{{ case.get_members|length }}</span>' +
+          '      <span class="badge badge-outlined release" style="border-width; 1px 1px 1px 0; border: 1px solid #323a45;">{{ case.release }}</span>' +
           '    </span>' +
           '  </label>' +
           '</span>'

cohorts/templates/cohorts/cohort_list.html

@@ -2,6 +2,7 @@
 
 {% load dict %}
 {% load humanize %}
+{% load variants_tags %}
 {% load cohorts_tags %}
 {% load projectroles_common_tags %}
 
@@ -90,6 +91,7 @@ <h4 class="card-header">
                       <a href="{{ case.get_absolute_url }}" class="badge-group" data-toggle="tooltip" data-html="true" title="From project <strong>{{ case.project.title }}</strong>, having {{ case.get_members|length }} individual(s)">
                         <span class="badge badge-secondary">{{ case.name }}</span>
                         <span class="badge badge-info">{{ case.get_members|length }}</span>
+                        <span class="badge badge-outlined release" style="border-width: 1px 1px 1px 0; border: 1px solid #323a45;">{{ case.release }}</span>
                       </a>
                   {% endfor %}
                   {% if not item|check_accessible_cases:user %}
@@ -105,7 +107,18 @@ <h4 class="card-header">
                       <span class="btn btn-sm btn-danger disabled"><i class="iconify" data-icon="mdi:trash-can"></i></span>
                       <span class="btn btn-sm btn-secondary disabled"><i class="iconify" data-icon="mdi:pencil"></i></span>
                     {% endif %}
-                    <a href="{% url 'variants:project-cases-filter-cohort' project=project.sodar_uuid cohort=item.sodar_uuid %}" class="btn btn-sm btn-primary"><i class="iconify" data-icon="mdi:filter"></i></a>
+
+
+                    {% same_release cases as cases_same_release %}
+                    {% if cases_same_release %}
+                      <a href="{% url 'variants:project-cases-filter-cohort' project=project.sodar_uuid cohort=item.sodar_uuid %}" class="btn btn-sm btn-primary"><i class="iconify" data-icon="mdi:filter"></i></a>
+                    {% else %}
+                      <span
+                        class="btn btn-sm btn-primary disabled"
+                        data-toggle="tooltip"
+                        title="Cannot filter cases with different genomes"
+                      ><i class="iconify" data-icon="mdi:filter"></i></span>
+                    {% endif %}
                   </span>
                 </td>
               </tr>

cohorts/templates/cohorts/cohort_update.html

@@ -112,6 +112,7 @@ <h5 class="mb-0">
           '    <span class="badge-group">' +
           '      <span class="badge badge-secondary">{{ label }}</span>' +
           '      <span class="badge badge-info members-count">{{ case.get_members|length }}</span>' +
+          '      <span class="badge badge-outlined release" style="border-width; 1px 1px 1px 0; border: 1px solid #323a45;">{{ case.release }}</span>' +
           '    </span>' +
           '  </label>' +
           '</span>'

config/settings/base.py

@@ -192,6 +192,51 @@
     logger.info("Enabling VarFishKioskUserMiddleware")
     MIDDLEWARE += ["varfish.utils.VarFishKioskUserMiddleware"]
 
+# Logging
+# ------------------------------------------------------------------------------
+
+# Custom logging level
+LOGGING_LEVEL = env.str("LOGGING_LEVEL", "DEBUG" if DEBUG else "ERROR")
+
+# List of apps to include in logging
+LOGGING_APPS = env.list(
+    "LOGGING_APPS",
+    default=["projectroles", "siteinfo", "sodarcache", "taskflowbackend", "timeline",],
+)
+
+# Path for file logging. If not set, will log only to console
+LOGGING_FILE_PATH = env.str("LOGGING_FILE_PATH", None)
+
+
+def set_logging(level=None):
+    if not level:
+        level = "DEBUG" if DEBUG else "ERROR"
+    app_logger_config = {
+        "level": level,
+        "handlers": ["console", "file"] if LOGGING_FILE_PATH else ["console"],
+        "propagate": True,
+    }
+    log_handlers = {
+        "console": {"level": level, "class": "logging.StreamHandler", "formatter": "simple",}
+    }
+    if LOGGING_FILE_PATH:
+        log_handlers["file"] = {
+            "level": level,
+            "class": "logging.FileHandler",
+            "filename": LOGGING_FILE_PATH,
+            "formatter": "simple",
+        }
+    return {
+        "version": 1,
+        "disable_existing_loggers": False,
+        "formatters": {"simple": {"format": "%(asctime)s [%(levelname)s] %(name)s: %(message)s"}},
+        "handlers": log_handlers,
+        "loggers": {a: app_logger_config for a in LOGGING_APPS},
+    }
+
+
+LOGGING = set_logging(LOGGING_LEVEL)
+
 # FIXTURE CONFIGURATION
 # ------------------------------------------------------------------------------
 # See: https://docs.djangoproject.com/en/dev/ref/settings/#std:setting-FIXTURE_DIRS
@@ -258,7 +303,7 @@
 
 # GENERAL CONFIGURATION
 # ------------------------------------------------------------------------------
-# Local time zone for this installation. Choices can be found here:
+# Local  zone for this installation. Choices can be found here:
 # http://en.wikipedia.org/wiki/List_of_tz_zones_by_name
 # although not all choices may be available on all operating systems.
 # In a Windows environment this must be set to your system time zone.
@@ -483,7 +528,7 @@
 # Enable submission of variants to CADD server.
 VARFISH_ENABLE_CADD_SUBMISSION = env.bool("VARFISH_ENABLE_CADD_SUBMISSION", default=False)
 # CADD version to use for for submission
-VARFISH_CADD_SUBMISSION_RELEASE = env.str("VARFISH_CADD_SUBMISSION_RELEASE", default="GRCh37-v1.6")
+VARFISH_CADD_SUBMISSION_VERSION = env.str("VARFISH_CADD_SUBMISSION_VERSION", default="v1.6")
 
 # Varfish: MutationTaster URL
 VARFISH_MUTATIONTASTER_REST_API_URL = env.str(

config/settings/test.py

@@ -78,6 +78,12 @@
     ]
 ]
 
+# Logging
+# ------------------------------------------------------------------------------
+
+LOGGING_LEVEL = env.str("LOGGING_LEVEL", "CRITICAL")
+LOGGING = set_logging(LOGGING_LEVEL)
+
 # Varfish: REST Services
 # ------------------------------------------------------------------------------
 

docs_manual/admin_config.rst

@@ -103,7 +103,7 @@ format, before starting your varfish instance (you can find more details `here <
 If you deploy varfish without docker, you can pass the file paths of your metadata.xml and key pair directly. Otherwise, make sure that you have included them
 into a single folder and added the corresponding folder to your ``docker-compose.yml`` (or add it as a ``docker-compose-overrrided.yml``), like in the following snippet.
 
-.. code-block:: yml
+.. code-block:: yaml
 
     varfish-web:
       ...

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()