Merge pull request #60 from mobidic/dev

Merge Dev

README.md

@@ -128,7 +128,7 @@ python insert_OMIM.py
 ### Launching the App
 
 Finally, to launch the app, run the following command:
-```
+```bash
 flask --app seal --debug run
 ```
 
@@ -146,6 +146,11 @@ flask --app seal --debug db upgrade
 pg_ctl -D ${PWD}/seal/seal.db -l ${PWD}/seal/seal.db.log start
 pg_ctl -D ${PWD}/seal/seal.db -l ${PWD}/seal/seal.db.log stop
 ```
+- Dump/Restore the database
+```bash
+pg_dump -O -C --if-exists --clean --inserts -d seal -x -F t -f seal.tar
+pg_restore -x -f seal.tar
+```
 
 # License
 

seal/__init__.py

@@ -19,8 +19,9 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 import os
-from datetime import timedelta
 import yaml
+from pathlib import Path
+from datetime import timedelta
 
 from flask import Flask, session, g, request, redirect, url_for
 from flask_apscheduler import APScheduler
@@ -33,7 +34,7 @@
 
 app = Flask(__name__)
 
-with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), "config.yaml"), "r") as config_file:
+with open(Path(app.root_path).joinpath("config.yaml"), "r") as config_file:
     config = yaml.safe_load(config_file)
 
 app.config.update(config['FLASK'])

seal/admin.py

@@ -29,7 +29,7 @@
 from seal import app, db, bcrypt
 from seal.models import (User, Team, Sample, Family, Variant, Comment_variant,
                          Comment_sample, Var2Sample, Filter, Transcript, Run,
-                         Region, Bed, Phenotype, Omim, History)
+                         Region, Bed, Phenotype, Omim, History, Clinvar)
 
 ###############################################################################
 
@@ -342,8 +342,9 @@ def validate_form(self, form):
         Variant,
         db.session,
         category="Variant",
-        column_searchable_list = ['chr', 'pos', 'ref', 'alt', 'annotations'],
-        column_editable_list = ['chr', 'pos', 'ref', 'alt', 'class_variant'],
+        column_searchable_list = ['chr', 'pos', 'ref', 'alt', 'class_variant', 'clinvar_VARID', 'clinvar_CLNSIG', 'clinvar_CLNSIGCONF', 'clinvar_CLNREVSTAT'],
+        column_editable_list = ['chr', 'pos', 'ref', 'alt', 'class_variant', 'clinvar_VARID', 'clinvar_CLNSIG', 'clinvar_CLNSIGCONF', 'clinvar_CLNREVSTAT'],
+        column_exclude_list = ['annotations'],
         form_excluded_columns = ['samples']
     )
 )
@@ -397,6 +398,14 @@ def validate_form(self, form):
     )
 )
 
+admin.add_view(
+    CustomView(
+        Clinvar,
+        db.session,
+        category="Analysis"
+    )
+)
+
 
 ###############################################################################
 

seal/forms.py

@@ -18,15 +18,19 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+import requests
+import pandas as pd
+
 from flask_wtf import FlaskForm
 from flask_wtf.file import FileField, FileAllowed
-from wtforms import StringField, PasswordField, SubmitField, BooleanField, ValidationError, TextAreaField, SelectMultipleField
-from wtforms.validators import DataRequired, Length, Email, Optional, EqualTo
 from flask_login import current_user
-from seal.models import User, Sample, Run, Team, Bed, Region
+from wtforms import (StringField, PasswordField, SubmitField, BooleanField,
+                     ValidationError, TextAreaField, SelectMultipleField,
+                     SelectField, DateField)
+from wtforms.validators import DataRequired, Length, Email, Optional, EqualTo
+
 from seal import bcrypt
-import pandas as pd
-import requests
+from seal.models import User, Sample, Run, Team, Bed, Region
 
 ################################################################################
 # Authentication
@@ -208,4 +212,21 @@ class SaveFilterForm(FlaskForm):
     submit = SubmitField('Add A New Filter')
 
 
+class UploadClinvar(FlaskForm):
+    version = DateField(
+        'Version',
+        validators=[DataRequired()], format='%Y-%m-%d'
+    )
+    genome_version = SelectField(
+        'Genome',
+        choices=[('grch37', 'grch37'), ('grch38', 'grch38')],
+        validators=[DataRequired()]
+    )
+    vcf_file = FileField(
+        'VCF',
+        validators=[DataRequired(), FileAllowed(['vcf', 'vcf.gz'])]
+    )
+    submit = SubmitField('Update Clinvar')
+
+
 ################################################################################

seal/models.py

@@ -30,8 +30,6 @@
 from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.dialects import postgresql
 
-
-
 ################################################################################
 # Authentication
 
@@ -136,6 +134,19 @@ def __str__(self):
         return self.teamname
 
 
+class Clinvar(db.Model):
+    version = db.Column(db.Integer, primary_key=True)
+    genome = db.Column(db.String(20), unique=False, nullable=False)
+    date = db.Column(db.TIMESTAMP(timezone=False), nullable=False, default=datetime.now())
+    current = db.Column(db.Boolean(), default=True, nullable=False)
+
+    def __repr__(self):
+        return f"Clinvar('{self.version}','{self.date}')"
+
+    def __str__(self):
+        return str(self.version)
+
+
 ################################################################################
 
 
@@ -155,6 +166,7 @@ class History(db.Model):
 class Sample(db.Model):
     id = db.Column(db.Integer, primary_key=True)
     samplename = db.Column(db.String(120), unique=False, nullable=False)
+    alias = db.Column(db.String(120), unique=False, nullable=True)
     status = db.Column(db.Integer, unique=False, nullable=False, default=0)
     affected = db.Column(db.Boolean(), default=False)
     index = db.Column(db.Boolean(), default=False)
@@ -211,6 +223,8 @@ class Run(db.Model):
     name = db.Column(db.String(50), unique=True, nullable=False)
     alias = db.Column(db.String(50), unique=False, nullable=True)
 
+    summary = db.Column(db.Text, unique=False, nullable=True)
+
     samples = relationship("Sample")
     reads = relationship("Read")
 
@@ -231,6 +245,11 @@ class Variant(db.Model):
     annotations = db.Column(db.JSON, nullable=True)
     comments = relationship("Comment_variant")
 
+    clinvar_VARID = db.Column(db.Integer, unique=False, nullable=True)
+    clinvar_CLNSIG = db.Column(db.String(500), unique=False, nullable=True)
+    clinvar_CLNSIGCONF = db.Column(db.String(500), unique=False, nullable=True)
+    clinvar_CLNREVSTAT = db.Column(db.String(500), unique=False, nullable=True)
+
     def __repr__(self):
         return f"Variant('{self.chr}','{self.pos}','{self.ref}','{self.alt}')"