Merge pull request #139 from bfrgoncalves/flowcraft_reports

Flowcraft reports

app/api.py

@@ -22,7 +22,7 @@
 from resources.postgres.reports import ReportsResource, \
     CombinedReportsResource, ReportsStrainResource, ReportsByProjectResource, \
     ReportInfoResource, ReportFilterResource, \
-    ReportsFileStrainResource, FilePathOnZipResource, SavedReportsResource
+    ReportsFileStrainResource, FilePathOnZipResource, SavedReportsResource, ReportByIdResource
 from resources.postgres.uploads import GetFilesResource, DownloadFilesResource
 from resources.ngs_onto.ngs_onto_projects import NGSOnto_ProjectUserResource, \
     NGSOnto_ProjectListUserResource
@@ -176,7 +176,7 @@
 api.add_resource(FilePathOnZipResource, '/api/v1.0/reports/files/')
 api.add_resource(CombinedReportsResource, '/api/v1.0/reports/combined')
 api.add_resource(SavedReportsResource, '/api/v1.0/reports/saved/')
-
+api.add_resource(ReportByIdResource, '/api/v1.0/reports/ids/')
 
 ################################# USER FILES ##################################
 

app/app_configuration.py

@@ -3,7 +3,7 @@
 import ldap
 
 from flask_security import Security, SQLAlchemyUserDatastore, login_required,\
-    current_user, utils, roles_required, user_registered, login_user, utils
+    current_user, utils, roles_required, user_registered, login_user
 from app import app, db, user_datastore, dbconAg,\
     security
 from app.models.models import Specie, User
@@ -77,6 +77,7 @@ def change_password():
                 return {"status": False}
 
         except ldap.INVALID_CREDENTIALS, e:
+            print e
             do_flash(*get_message('INVALID_PASSWORD'))
             return {"status": False}
 

app/models/models.py

@@ -125,6 +125,7 @@ def try_login(email, password):
         try:
             conn.simple_bind_s("cn="+email+",ou=users,"+baseDN, password)
         except Exception as e:
+            print e
             return False
 
         search_filter = "uid="+email

app/resources/jobs/jobs.py

@@ -334,6 +334,8 @@ def post(self):
                                   user_id, json_data["task"],
                                   parameters_json["species"], overwrite)
 
+        print is_added
+
         return True
 
 
@@ -559,6 +561,7 @@ def get(self):
                         file2Path.append(
                             '/'.join(r["file_4"].split("/")[-3:-1]))
                 except Exception as p:
+                    print p
                     file2Path = []
 
             except Exception as e:
@@ -719,9 +722,6 @@ def get(self):
 
         args = nextflow_logs_get_parser.parse_args()
 
-        til_storage = "/".join(current_user.homedir.split("/")[0:-3])
-        content = ""
-
         project = db.session.query(Project).filter(
             Project.id == args.project_id).first()
 
@@ -770,15 +770,23 @@ def get(self):
 
         args = inspect_get_parser.parse_args()
 
-        request = requests.get(os.path.join(JOBS_ROOT, "inspect"),
-                                params={
-                                    'homedir': current_user.homedir,
-                                    'pipeline_id': args.pipeline_id,
-                                    'project_id': args.project_id,
-                                }
-                                )
+        out = {"message": "Inspect feature for this strain."}
 
-        out = request.json()
+        projectObject = db.session.query(Project).filter(args.project_id == Project.id).first()
+
+        if projectObject:
+            userObject = db.session.query(User).filter(User.id == projectObject.user_id).first()
+
+            if userObject:
+                request = requests.get(os.path.join(JOBS_ROOT, "inspect"),
+                                        params={
+                                            'homedir': userObject.homedir,
+                                            'pipeline_id': args.pipeline_id,
+                                            'project_id': args.project_id,
+                                        }
+                                        )
+
+                out = request.json()
 
         return out
 

app/resources/ngs_onto/ngs_onto_users.py

@@ -60,7 +60,8 @@ def post(self):
             dedicateddbconAg.commit()
             dedicateddbconAg.close()
             return 201
-        except:
+        except Exception as e:
+            print e
             dedicateddbconAg.rollback()
             dedicateddbconAg.close()
             return 404

app/resources/postgres/reports.py

@@ -24,6 +24,12 @@
 report_get_parser.add_argument('species_id', dest='species_id', type=str,
                                required=False, help="Species ID")
 
+# Defining post arguments parser
+report_post_id_parser = reqparse.RequestParser()
+
+report_post_id_parser.add_argument('job_ids', dest='job_ids', type=str,
+                               required=False, help="job identifier")
+
 # Defining projects get arguments parser
 report_get_project_parser = reqparse.RequestParser()
 
@@ -293,11 +299,52 @@ def post(self):
             .all()
 
         for x in reports:
+            if "reportJson" in x.report_data.keys():
+                if "cagao" in x.report_data["reportJson"]:
+                    del x.report_data["reportJson"]["cagao"]
+
             reports_to_send.append(x.report_data)
 
         return reports_to_send, 200
 
 
+class ReportByIdResource(Resource):
+    """
+    Class to get reports by applying filters
+    """
+
+    # @login_required
+    def post(self):
+        """Reports with filters
+
+        Returns the projects filtered according to a list of selected projet
+        identifiers and strain identifiers.
+
+        Returns
+        -------
+        list: list of reports
+        """
+
+        args = report_post_id_parser.parse_args()
+
+        job_ids = args.job_ids.split(",")
+
+        reports_to_send = []
+
+        for job in job_ids:
+            j = job.split("-")
+
+            report = db.session.query(Report)\
+                .filter(Report.project_id == j[0],
+                        Report.pipeline_id == j[1],
+                        Report.process_position == j[2]).first()
+
+            if report:
+                reports_to_send.append(report.report_data)
+
+        return reports_to_send, 200
+
+
 class ReportsByProjectResource(Resource):
     """
     Class to get reports by project

app/resources/postgres/uploads.py

@@ -35,6 +35,7 @@ def get(self):
         try:
             return request.json(), 200
         except Exception as e:
+            print e
             return False, 200
 
 

app/resources/postgres/users.py

@@ -189,8 +189,6 @@ def get(self):
         project_dir = os.path.join(current_user.homedir, "jobs",
                                    project_id+"-*")
 
-        print instStorage
-
         # Get size of homedir
         proc = subprocess.Popen(["du", "-sh", "-B1", current_user.homedir],
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -209,6 +207,7 @@ def get(self):
                     try:
                         out3 += os.path.getsize(fp)
                     except Exception as e:
+                        print e
                         print "error loading " + fp
 
         proc = subprocess.Popen(["df", "-Ph", "-B1", current_user.homedir],

app/resources/postgres/workflows.py

@@ -127,7 +127,7 @@ def get(self):
         workflows = db.session.query(Workflow).all()
 
         if not workflows:
-            abort(404, message="No workflows are available".format(id))
+            abort(404, message="No workflows are available")
         return workflows, 200
 
 
@@ -253,6 +253,7 @@ def post(self):
                     loaded_steps = json.loads(protocol.steps.replace("'", '"'))
                     list_tags.append(loaded_steps["Nextflow Tag"])
                 except Exception as e:
+                    print e
                     return {"content": "Protocol with errors. Please create "
                                        "another protocol to use when building this workflow."}