Adding mutation data to CAMEL database

.docker/DB.Dockerfile

@@ -1,3 +1,3 @@
-FROM mariadb:latest
+FROM mysql:latest
 
 COPY .docker/CAMEL.sql /docker-entrypoint-initdb.d/CAMEL.sql

.docker/README.md

@@ -124,7 +124,13 @@ To verify that it works.
    5.4. `docker-compose down`
 
 6. We assume that you have a database dump of MySQL in the root folder. 
-   It could have been created via `mysqldump --add-drop-table -u admin -p`cat /etc/psa/.psa.shadow` dbname > dbname.sql`
+   It could have been created via `mysqldump --add-drop-table -u admin -p` cat /etc/psa/.psa.shadow` dbname > dbname.sql`
+
+   In CAMEL's current state, to run `mysqldump` from the Dockerized MariaDB, try:
+
+   `docker exec [CONTAINER ID] [path to mysqldump executible] -u [USERNAME] --password=[PASSWORD] CAMEL > CAMEL.sql`
+   or
+   `docker exec 16b028adef6f mysqldump -u camel --password=abcdef CAMEL > CAMEL.sql`
 
    This database dump could be imported in the database server once started by using 
    `mysql -u admin -p`cat /etc/psa/.psa.shadow` -h camel-database dbname < dbname.sql`

.gitignore

@@ -3,3 +3,5 @@ camel.conf
 public/app/app.config.js
 __pycache__
 auth/.htpasswd
+.docker/.DS_Store
+.DS_Store

api/Camel/__init__.py

@@ -41,9 +41,11 @@ def __init__(self):
 from Camel.auth import Auth, Logout
 from Camel.experiment import Experiment, ExperimentList
 from Camel.field import Field, FieldList
+from Camel.field_mut import FieldMut, FieldMutList
 from Camel.reference import Reference, ReferenceList
 from Camel.attachment import Attachment
 from Camel.pubmed import PubMed
+from Camel.mutation import Mutation, MutationList
 
 ## Init Flask App
 app = Flask(__name__)
@@ -54,8 +56,12 @@ def __init__(self):
 api.add_resource(Logout, '/auth/logout')
 api.add_resource(ExperimentList, '/experiment')
 api.add_resource(Experiment, '/experiment/<int:id>')
+api.add_resource(MutationList, '/mutation')
+api.add_resource(Mutation, '/mutation/<int:id>')
 api.add_resource(FieldList, '/field')
 api.add_resource(Field, '/field/<string:id>')
+api.add_resource(FieldMutList, '/field_mut')
+api.add_resource(FieldMut, '/field_mut/<string:id>')
 api.add_resource(ReferenceList, '/reference')
 api.add_resource(Reference, '/reference/<int:id>')
 api.add_resource(Attachment, '/attachment')

api/Camel/auth.py

@@ -30,10 +30,10 @@ def wrapped_endpoint(self, *args, **kwargs):
             'WWW-Authenticate': 'Basic realm="Login Required"'
         })
 
-        if 'AuthToken' not in request.headers:
+        if 'Authheader' not in request.headers:
             return unauthorised
 
-        token = request.headers['AuthToken']
+        token = request.headers['Authheader']
         db = db_connect(config)
         sql = "SELECT `token` from `sessions` WHERE `token` = %(token)s"
         c = db.cursor()

api/Camel/field_mut.py

@@ -0,0 +1,193 @@
+from pathlib import Path
+import shutil
+
+from flask_restful import request, reqparse
+from MySQLdb.cursors import DictCursor
+
+from Camel import CamelResource, config
+from Camel.auth import login_required
+
+class FieldMutList(CamelResource):
+
+    def __init__(self):
+        self.reqparse = reqparse.RequestParser()
+
+        ##POST arguments
+        self.reqparse.add_argument('title', required = True, type = str, location = 'json')
+        self.reqparse.add_argument('unit', required = True, type = str, location = 'json')
+        self.reqparse.add_argument('description', required = True, type = str, location = 'json')
+        self.reqparse.add_argument('type_column', required = True, type = str, location = 'json')
+        self.reqparse.add_argument('options', required = True, type = str, location = 'json')
+        self.reqparse.add_argument('link', required = True, type = int, location = 'json')
+        self.reqparse.add_argument('required', required = True, type = int, location = 'json')
+        self.reqparse.add_argument('group', required = True, type = int, location = 'json')
+        self.reqparse.add_argument('weight', required = True, type = int, location = 'json')
+        self.reqparse.add_argument('group_id', required = True, type = int, location = 'json')
+
+        super(FieldMutList, self).__init__()
+
+    def retrieveFieldData(self):
+        sql = ("SELECT `id`, `title`, `unit`, `description`, `type_column`, `options`, `link`, `required`, `weight`, `group`, `group_id` "
+               "FROM `fields_mut` "
+               "ORDER BY `weight`")
+
+        c = self.db.cursor(DictCursor)
+        c.execute(sql)
+        rows = c.fetchall()
+        c.close()
+        return rows
+
+    def get(self):        
+        rows = self.retrieveFieldData()
+        return rows
+
+
+    @login_required
+    def post(self):
+        sql = ("INSERT INTO `fields` (`title`, `unit`, `description`, `type_column`, `options`, `link`, `required`, `weight`, `group`, `group_id`) "
+               "VALUES (%(title)s, %(unit)s, %(description)s, %(type_column)s, %(options)s, %(link)s, %(required)s, %(weight)s, %(group)s, %(group_id)s)")
+
+        args = self.reqparse.parse_args()
+        c = self.db.cursor()
+        c.execute(sql, args)
+        newid = c.lastrowid
+        self.db.commit()
+        c.close()
+
+        args['id'] = newid
+        return args, 201
+
+
+class FieldMut(CamelResource):
+    def __init__(self):
+        self.reqparse = reqparse.RequestParser()
+
+        ##PUT arguments
+        self.reqparse.add_argument('title', type = str, location = 'json')
+        self.reqparse.add_argument('unit', type = str, location = 'json')
+        self.reqparse.add_argument('description', type = str, location = 'json')
+        self.reqparse.add_argument('options', type = str, location = 'json')
+        self.reqparse.add_argument('link', type = int, location = 'json')
+        self.reqparse.add_argument('required', type = int, location = 'json')
+        self.reqparse.add_argument('group', type = int, location = 'json')
+        self.reqparse.add_argument('weight', type = int, location = 'json')
+        self.reqparse.add_argument('group_id', type = int, location = 'json')
+
+        ##Optional GET argument
+        self.reqparse.add_argument('timeline', type = int, help = 'timeline is an optional flag [0|1]', location= 'args')
+
+        super(FieldMut, self).__init__()
+
+
+    def get(self, id):
+        self.reqparse.parse_args()
+
+        sql = ("SELECT `id`, `title`, `unit`, `type_column` "
+               "FROM `fields_mut` ")
+
+        tokens = {}
+        if id.isnumeric():
+            sql += "WHERE `id` = %(id)s"
+            tokens['id'] = id
+        else:
+            sql += "WHERE `title` = %(title)s"
+            tokens['title'] = id
+
+        c = self.db.cursor(DictCursor)
+        c.execute(sql, tokens)
+        field_props = c.fetchone()
+        c.close()
+
+        type_col = field_props['type_column']
+
+        if 'timeline' not in request.args or not request.args['timeline'] == '1':
+            sql = ("SELECT ef.`{type_col}` value, COUNT(*) number "
+                   "FROM `experiments_fields` ef "
+                   "WHERE ef.`field_id` = %(field_id)s "
+                   "GROUP BY `value` "
+                   "ORDER BY `number` DESC").format(type_col=type_col)
+
+        else:
+            sql = ("SELECT ef.`{type_col}` value, r.`year`, COUNT(*) number "
+                   "FROM `experiments_fields` ef "
+                   "JOIN `experiments_references` er ON er.`experiment_id` = ef.`experiment_id` "
+                   "JOIN `references` r ON r.`id` = er.`reference_id` "
+                   "WHERE ef.`field_id` = %(field_id)s "
+                   "GROUP BY `value`, `year` "
+                   "ORDER BY `year`").format(type_col=type_col)
+
+        tokens = {}
+        tokens['field_id'] = field_props['id'];
+
+        c = self.db.cursor(DictCursor)
+        print(sql)        
+        c.execute(sql, tokens)
+        field_stats = c.fetchall()
+        field_props['values'] = field_stats;
+        c.close()                
+
+        return field_props
+
+    @login_required
+    def put(self, id):
+        sql = "SELECT count(*) FROM `fields_mut` WHERE `id` = %(id)s"
+        c = self.db.cursor()
+        c.execute(sql, {'id': id})
+        res = c.fetchone()
+        c.close()
+        if res[0] != 1:
+            return "No such field"
+
+        args = self.reqparse.parse_args()
+        if request.json:
+            sql = "UPDATE `fields_mut` SET "
+            updates = []
+            for arg_key in request.json:
+                if arg_key in args:
+                    updates.append("`{arg_key}` = %({arg_key})s ".format(arg_key=arg_key))
+            sql+=', '.join(updates)
+            sql+="WHERE id = %(id)s"
+            c = self.db.cursor()
+            tokens = args
+            tokens['id'] = id
+            c.execute(sql, tokens)
+            self.db.commit()
+            c.close()
+
+        return "Update succesful", 204
+
+    @login_required
+    def delete(self, id):
+        ## Does field exist?
+        sql = "SELECT `id`, `type_column` FROM `fields_mut` WHERE `id` = %(id)s"
+        c = self.db.cursor()
+        c.execute(sql, {'id': id})
+        res = c.fetchall()
+
+        if len(res) != 1:
+            return "No such field"
+        else:
+            type_column = res[0][1]
+
+        ## Clean up ATTACH field
+        if type_column == 'value_ATTACH':
+            upload_conf = config['uploads']            
+            upload_path = Path(upload_conf['PATH'])
+            sql = "SELECT `experiment_id` FROM `experiments_fields` WHERE `field_id` = %(id)s"
+            c.execute(sql, {'id': id})
+            res = c.fetchall()
+            for row in res:
+                exp_id = row[0]
+                attachment_dir = upload_path.joinpath(str(exp_id), str(id))
+                shutil.rmtree(attachment_dir, ignore_errors=True)
+
+        ## Delete from db
+        sql = "DELETE FROM `fields_mut` WHERE `id` = %(id)s"
+
+        c.execute(sql, {'id': id})
+
+        self.db.commit()
+        c.close()
+
+        return "Field deleted", 204
+