From d0792b683b19d039b0e20b8622542248137ab80e Mon Sep 17 00:00:00 2001
From: Christos Kopanos <christos.kopanos@saphetor.com>
Date: Wed, 11 Apr 2018 16:43:18 +0300
Subject: [PATCH] Fixed cosmic licensed data model and added acmg annotations
 model

---
 setup.py                                |  2 +-
 varsome_api/models/elements/__init__.py |  1 +
 varsome_api/models/elements/acmg.py     | 42 +++++++++++++++++++++++++
 varsome_api/models/elements/sanger.py   |  5 ++-
 varsome_api/models/variant.py           |  3 +-
 5 files changed, 49 insertions(+), 4 deletions(-)
 create mode 100644 varsome_api/models/elements/acmg.py

diff --git a/setup.py b/setup.py
index c599bc5..c77e73f 100755
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 import sys
 from os import path
 
-VERSION = (1, 0, '0b1')
+VERSION = (1, 1, '0b1')
 __version__ = VERSION
 __versionstr__ = '.'.join(map(str, VERSION))
 
diff --git a/varsome_api/models/elements/__init__.py b/varsome_api/models/elements/__init__.py
index 276d4c7..b1f5852 100755
--- a/varsome_api/models/elements/__init__.py
+++ b/varsome_api/models/elements/__init__.py
@@ -15,3 +15,4 @@
 from .uniprot import *
 from .wustl import *
 from .gwas import *
+from .acmg import *
diff --git a/varsome_api/models/elements/acmg.py b/varsome_api/models/elements/acmg.py
new file mode 100644
index 0000000..7650b8d
--- /dev/null
+++ b/varsome_api/models/elements/acmg.py
@@ -0,0 +1,42 @@
+# Copyright 2018 Saphetor S.A.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from jsonmodels import models, fields
+
+__author__ = "ckopanos"
+
+
+class ACMGClassification(models.Base):
+    met_criteria = fields.BoolField()
+    name = fields.StringField(help_text="ACMG Classification Name")
+    user_explain = fields.ListField(items_types=(str,), help_text="Criteria explanation", required=False,
+                                    nullable=True)
+
+
+class ACMGRule(models.Base):
+    pathogenic_subscore = fields.StringField(required=False, nullable=True)
+    benign_subscore = fields.StringField(required=False, nullable=True)
+    verdict = fields.StringField(required=False, nullable=True)
+
+
+class ACMGVerdict(models.Base):
+    classifications = fields.ListField(items_types=(str,), help_text="Classification names", required=False,
+                                       nullable=True)
+    ACMG_rules = fields.EmbeddedField(ACMGRule)
+
+
+class ACMG(models.Base):
+    classifications = fields.ListField(required=False, items_types=(ACMGClassification,),
+                                       help_text="ACMG Classifications")
+    verdict = fields.EmbeddedField(ACMGVerdict, nullable=True, required=False, help_text="ACMG Verdict")
diff --git a/varsome_api/models/elements/sanger.py b/varsome_api/models/elements/sanger.py
index de8a12f..6268da7 100755
--- a/varsome_api/models/elements/sanger.py
+++ b/varsome_api/models/elements/sanger.py
@@ -40,7 +40,7 @@ class CosmicLicensedDrugEntry(models.Base):
 
 class CosmicLicensedDetails(models.Base):
     entry_type = fields.StringField(help_text="Entry type", required=False, nullable=True)
-    cosmic_id = fields.ListField(items_types=(str,), help_text="Cosmic ID", required=False, nullable=True)
+    cosmic_id = fields.ListField(items_types=(str, dict,), help_text="Cosmic ID", required=False, nullable=True)
     pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False,
                                           nullable=True)
     histology_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False,
@@ -84,6 +84,9 @@ class CosmicLicensedDetails(models.Base):
 class ComsicPublicDetails(models.Base):
     num_samples = fields.IntField(help_text='Number of samples')
     id = fields.StringField(help_text='Cosmic ID')
+    is_consistent = fields.BoolField(help_text='Cosmic ID is consistent across databases')
+
+
 
 
 class CosmicPublic(models.Base):
diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py
index bdc19a2..fbb02ee 100755
--- a/varsome_api/models/variant.py
+++ b/varsome_api/models/variant.py
@@ -11,8 +11,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
 from .fields import DictField
 from .elements import *
 
@@ -58,6 +56,7 @@ class AnnotatedVariant(models.Base):
     uniprot_variants = fields.ListField(required=False, items_types=(UniprotVariants,), help_text="UniProt variants")
     wustl_civic = fields.ListField(required=False, items_types=(Civic,), help_text="CIViC")
     gwas = fields.ListField(required=False, items_types=(GWAS,), help_text="GWAS")
+    acmg_annotation = fields.EmbeddedField(ACMG, required=False, nullable=True, help_text="ACMG Annotations")
 
     @property
     def genes(self):