Develop

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": "flask/bin/python2.7"
+}

app/models/models.py

@@ -226,6 +226,7 @@ class Project(db.Model):
     is_removed = db.Column(db.String(255))
     description = db.Column(db.Text())
     timestamp = db.Column(db.DateTime)
+    last_update_timestamp = db.Column(db.DateTime)
     user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
     pipelines = db.relationship('Pipeline', backref='project', lazy='dynamic')
     strains = db.relationship('Strain', secondary=projects_strains,
@@ -376,6 +377,8 @@ class Strain(db.Model):
     id = db.Column(db.Integer(), primary_key=True)
     name = db.Column(db.String(255), unique=True)
     timestamp = db.Column(db.DateTime)
+    update_timestamp = db.Column(db.DateTime)
+    delete_timestamp = db.Column(db.DateTime)
     strain_metadata = db.Column(JSON)
     fields = db.Column(JSON)
     species_id = db.Column(db.Integer, db.ForeignKey('species.id'))

app/resources/jobs/checks.py

@@ -53,6 +53,7 @@ def get(self):
                 print e
                 return False
 
+
         return True
 
 

app/resources/postgres/projects.py

@@ -48,7 +48,9 @@
     'uri': fields.Url('user_single_project', absolute=True),
     'species_id': fields.String,
     'is_removed': fields.String,
-    'username': fields.String
+    'username': fields.String,
+    'number_strains_change': fields.Integer,
+    'strains_expire': fields.List(fields.String)
 }
 
 project_fields = {
@@ -303,6 +305,16 @@ def get(self, id):
                 .filter(project.user_id == User.id).first()
 
             project.username = user.username
+            count = 0
+            project.strains_expire = []
+
+
+            for strain in project.strains:
+                if strain.delete_timestamp != None:
+                    if strain.delete_timestamp > project.timestamp:
+                        count+=1
+                    project.strains_expire.append(strain.name)  
+            project.number_strains_change = count
 
         return projects, 200
 

app/resources/postgres/strains.py

@@ -12,6 +12,7 @@
 
 # Defining post arguments parser
 
+
 strain_project_parser = reqparse.RequestParser()
 strain_project_parser.add_argument('strainID', dest='strainID', type=str,
                                    required=False, help="Strain identifier")
@@ -60,7 +61,10 @@
     'classifier': fields.String,
     'fq_location': fields.String,
     'has_files': fields.String,
-    'Accession': fields.String
+    'Accession': fields.String,
+    'delete_timestamp': fields.String,
+    'update_timestamp': fields.String,
+    'strainsIDs': fields.List(fields.String)
 }
 
 strain_fields_project = {
@@ -160,6 +164,14 @@ def get(self):
         else:
             strains = db.session.query(Strain).all()
 
+        strains_aux = list(strains)
+
+        for strain in strains:
+          if strain.delete_timestamp != None:
+                strains_aux.remove(strain)
+
+        strains = strains_aux 
+
         for strain in strains:
             strain.file_1 = json.loads(strain.strain_metadata)["File_1"]
             strain.file_2 = json.loads(strain.strain_metadata)["File_2"]
@@ -288,11 +300,72 @@ def put(self):
             for key, val in args.iteritems():
                 strain_metadata[key] = val
 
+            if "Accession" in args:
+
+                metadata = json.loads(strain.strain_metadata)
+
+                if metadata["Accession"] != args["Accession"]:
+
+                    strain_specie_name = database_correspondece.keys()[strain.species_id - 1]
+
+                    strain_specie = database_correspondece[strain_specie_name]
+
+                    result = db.session.query(strain_specie).filter(strain_specie.strain_metadata['strainID'].astext == metadata["Accession"]).first()
+
+                    if not result:
+                        abort(404, message="An error as occurried")
+
+                    strain.update_timestamp = datetime.datetime.utcnow()
+
             strain.strain_metadata = json.dumps(strain_metadata)
+
             db.session.commit()
 
             return strain, 201
 
+    @login_required
+    @marshal_with(strain_fields)
+    def delete(self):
+        """Remove strain 
+
+        This method allows removing a strain. Requires the
+        strain name and the project id.
+
+        Parameters
+        ----------
+        id: str
+            project identifier
+
+        Returns
+        -------
+
+        """
+
+
+        args = request.data
+
+        obj = json.loads(args) 
+
+        strains_ids = list(obj.values())[0]
+
+        if not current_user.is_authenticated:
+            abort(403, message="No permissions")
+
+        for strainId in strains_ids:
+            strain = db.session.query(Strain).filter(Strain.id == strainId).first()
+
+            if not strain:
+                abort(404, message="No strain available")
+
+            if strain.user_id != current_user.id:
+                abort(404, message="No permissions")
+
+            strain.delete_timestamp = datetime.datetime.utcnow()
+
+        db.session.commit()
+
+        return 200
+
 
 class StrainsByNameResource(Resource):
     """

app/static/controllers/js_objects/metadata.js

@@ -50,7 +50,8 @@ const Metadata = () => {
         "Project Name":"project_name",
         "Classifier":"classifier",
         "Accession": "Accession",
-        "Timestamp":"timestamp"
+        "Timestamp":"timestamp",
+        "Strain_State":"Strain_State"
     };
 
     //Conversion from the metadata fields stored in the db to how we want to see them on a table (Reverse)
@@ -76,18 +77,19 @@ const Metadata = () => {
         "project_name": "Project Name",
         "classifier": "Classifier",
         "Accession": "Accession",
-        "timestamp": "Timestamp"
+        "timestamp": "Timestamp",
+        "Strain_State":"Strain_State"
     };
 
     //The minimum headers to be seen on a table
     const minimal_headers = [
         "Strain Name", "Received Date", "Source", "Additional Info", "File 1",
         "Primary", "Sampling Date", "Owner", "Case ID", "Submitter", "File 2",
-        "Location", "Accession", "Timestamp"];
+        "Location", "Accession", "Timestamp", "Strain_State"];
 
     const default_headers = [
-        "Strain Name", "Received Date", "Source", "Sampling Date", "Location",
-        "Sample", "Run Identifier", "Project Name", "Classifier", "Accession", "Timestamp"];
+        "Strain Name", "Received Date", "Source", "Sampling Date", "Location","Owner",
+        "Sample", "Run Identifier", "Project Name", "Classifier", "Accession", "Timestamp","Strain_State"];
 
     return {
 

app/static/controllers/js_objects/objects_utils.js

@@ -53,7 +53,11 @@ const Objects_Utils = (single_project, $sc) => {
     const format_analysis = (d, table_id) => {
         // `d` is the original data object for the row
 
-        $("#" + d.strainID + "_table").remove();
+
+        let strain_id = d.strainID;
+        strain_id = strain_id.replace(/(.*?) <i.*/i, "$1")  ;
+
+        $("#" + strain_id + "_table").remove();
 
         let tr_string = "";
 
@@ -148,7 +152,8 @@ const Objects_Utils = (single_project, $sc) => {
         }
 
         if (table_id === "modify_strains_table" || table_id === "reports_trees_table") {
-            selection_style = "single";
+            //selection_style = "single";
+            selection_style = "multi";
         }
         else {
             selection_style = "multi";
@@ -745,7 +750,7 @@ const Objects_Utils = (single_project, $sc) => {
 
             $("#" + table_id + " thead").append(create_table_headers(table_headers, has_analysis, table_id));
             $("#" + table_id + " tfoot > tr").remove();
-            $("#" + table_id + " tfoot").append(create_table_headers(table_headers, has_analysis, table_id));
+            //$("#" + table_id + " tfoot").append(create_table_headers(table_headers, has_analysis, table_id));
 
 
             callback();

app/static/controllers/js_objects/projects_table.js

@@ -102,13 +102,25 @@ const Projects_Table = (CURRENT_PROJECT_ID, CURRENT_PROJECT, $http) => {
                                         ' fa-unlock"></i></div>';
                                 }
 
+                                if(d.number_strains_change > 0)
+                                {
+                                    icon = "<i class='fa fa-ban' style='color:#DC143C;'></i>";
+                                        d.Project_State= icon + "<strong style='color:#DC143C;'> - Outdated </strong>";
+
+                                }else{
+                                    icon = "<i class='fa fa-check' style='color:#006400;'></i>";
+                                    d.Project_State= icon + "<strong style='color:#006400;'> - Up-to-date </strong>";
+                                }
+
+
                                 other_projects.push({
                                     name: d.name,
                                     description: d.description,
                                     date: d.timestamp.split(" ").slice(0, 4).join(' '),
                                     id: d.id,
                                     username: d.username,
-                                    lockStatus: lockStatus
+                                    lockStatus: lockStatus,
+                                    Project_State:d.Project_State
                                 });
                             }
                         });
@@ -138,13 +150,32 @@ const Projects_Table = (CURRENT_PROJECT_ID, CURRENT_PROJECT, $http) => {
                                         ' fa-unlock"></i></div>';
                                 }
 
+
+                                let strain_ex = d.name;
+                                if(d.number_strains_change > 0)
+                                {
+                                    icon = "<i class='fa fa-ban' style='color:#DC143C;'></i>";
+                                        d.Project_State= icon + "<strong style='color:#DC143C;'> - Outdated </strong>";
+                                    if(d.strains_expire.includes(d.name))
+                                    {
+
+                                        strain_ex += " " + "<i class=\"fa fa-exclamation-triangle\" title=\"Esta strain foi removida ou alterada.\" style=\"color:orange\"></i>";
+                                    }
+                                }else{
+                                    icon = "<i class='fa fa-check' style='color:#006400;'></i>";
+                                    d.Project_State= icon + "<strong style='color:#006400;'> - Up-to-date </strong>";
+                                }
+
                                 projects.push({
-                                    name: d.name,
+                                    name: strain_ex,
                                     description: d.description,
                                     date: d.timestamp.split(" ").slice(0, 4).join(' '),
                                     id: d.id,
                                     username: d.username,
-                                    lockStatus: lockStatus
+                                    lockStatus: lockStatus,
+                                    number_strains_change: d.number_strains_change,
+                                    strains_expire: d.strains_expire,
+                                    Project_State:d.Project_State
                                 });
                             }
                         });
@@ -180,13 +211,16 @@ const Projects_Table = (CURRENT_PROJECT_ID, CURRENT_PROJECT, $http) => {
                         ' style="width:100%;text-align:center;"><i class="fa' +
                         ' fa-unlock"></i></div>';
 
+                     let  icon = "<i class='fa fa-check' style='color:#006400;'></i>";
+
                     projects.push({
                         name: response.data.name,
                         description: response.data.description,
                         date: response.data.timestamp.split(" ").slice(0, 4).join(' '),
                         id: response.data.id,
                         username: response.data.username,
-                        lockStatus: lockStatus
+                        lockStatus: lockStatus,
+                        Project_State:icon+ "<strong style='color:#006400;'> - Up-to-date </strong>"
                     });
 
                     $('#newProjectModal').modal('hide');