Merge remote-tracking branch 'origin/chore/study-progress' into staging-500-error

crc/models/study.py

@@ -70,6 +70,7 @@ class StudyModel(db.Model):
     on_hold = db.Column(db.Boolean, default=False)
     proposal_name = db.Column(db.String, nullable=True)
     short_name = db.Column(db.String, nullable=True)
+    progress = db.Column(db.Integer, nullable=True)
 
     def update_from_protocol_builder(self, study: ProtocolBuilderCreatorStudy, user_id):
         self.title = study.TITLE
@@ -213,8 +214,8 @@ class Study(object):
                  comment="",
                  sponsor="", ind_number="", categories=[],
                  files=[], approvals=[], enrollment_date=None, events_history=[],
-                 last_activity_user="", last_activity_date=None, create_user_display="",
-                 primary_investigator="", **argsv):
+                 primary_investigator="",
+                 last_activity_user="",last_activity_date =None,create_user_display="", progress=0, **argsv):
         self.id = id
         self.user_uid = user_uid
         self.create_user_display = create_user_display
@@ -238,6 +239,7 @@ class Study(object):
         self.short_name = short_name
         self.proposal_name = proposal_name
         self.primary_investigator = primary_investigator
+        self.progress = progress
 
     @classmethod
     def from_model(cls, study_model: StudyModel):
@@ -301,13 +303,14 @@ class StudySchema(ma.Schema):
     proposal_name = fields.String(allow_none=True)
     review_type = fields.Integer(allow_none=True)
     primary_investigator = fields.String(allow_none=True)
+    progress = fields.Integer(allow_none=True)
 
     class Meta:
         model = Study
         additional = ["id", "title", "short_title", "last_updated", "user_uid",
                       "sponsor", "ind_number", "files", "enrollment_date",
                       "create_user_display", "last_activity_date", "last_activity_user",
-                      "events_history", "short_name", "proposal_name", "primary_investigator"]
+                      "events_history", "short_name", "proposal_name", "progress", "primary_investigator"]
         unknown = INCLUDE
 
     @marshmallow.post_load

crc/services/study_service.py

@@ -65,16 +65,20 @@ class StudyService(object):
             studies.append(study)
         return studies
 
+
     @staticmethod
+    @timeit
     def get_study(study_id, categories: List[WorkflowSpecCategory], study_model: StudyModel = None,
                   master_workflow_results=None):
         """Returns a study model that contains all the workflows organized by category.
         Pass in the results of the master workflow spec, and the status of other workflows will be updated."""
-
+        last_time = firsttime()
         if not study_model:
             study_model = session.query(StudyModel).filter_by(id=study_id).first()
         study = Study.from_model(study_model)
+        last_time = sincetime("from model", last_time)
         study.create_user_display = LdapService.user_info(study.user_uid).display_name
+        last_time = sincetime("user", last_time)
         last_event: TaskEventModel = session.query(TaskEventModel) \
             .filter_by(study_id=study_id, action='COMPLETE') \
             .order_by(TaskEventModel.date.desc()).first()
@@ -84,11 +88,13 @@ class StudyService(object):
         else:
             study.last_activity_user = LdapService.user_info(last_event.user_uid).display_name
             study.last_activity_date = last_event.date
+        last_time = sincetime("task_events", last_time)
         study.categories = categories
         files = UserFileService.get_files_for_study(study.id)
         files = (File.from_models(model, UserFileService.get_file_data(model.id),
                                   DocumentService.get_dictionary()) for model in files)
         study.files = list(files)
+        last_time = sincetime("files", last_time)
         if study.status != StudyStatus.abandoned:
             for category in study.categories:
                 workflow_metas = StudyService._get_workflow_metas(study_id, category)
@@ -99,13 +105,29 @@ class StudyService(object):
                     category_meta = StudyService._update_status_of_category_meta(master_workflow_results, category)
                 category.workflows = workflow_metas
                 category.meta = category_meta
+        last_time = sincetime("categories", last_time)
 
         if study.primary_investigator is None:
             associates = StudyService().get_study_associates(study.id)
             for associate in associates:
                 if associate.role == "Primary Investigator":
                     study.primary_investigator = associate.ldap_info.display_name
+        # Calculate study progress and return it as a integer out of a hundred
+        last_time = sincetime("PI", last_time)
+        completed_wfs = 0
+        total_wfs = 0
+        for category in study.categories:
+            for workflow in category.workflows:
+                total_wfs +=1
+                if workflow.status == WorkflowStatus.complete:
+                    completed_wfs += 1
+        if total_wfs > 0:
+            study.progress = int((completed_wfs/total_wfs)*100)
+        else:
+            study.progress = 0
         return study
+        last_time = sincetime("progress", last_time)
+
 
     @staticmethod
     def _get_workflow_metas(study_id, category):
@@ -267,6 +289,7 @@ class StudyService(object):
             g.doc_statuses[study_id] = StudyService.__get_documents_status(study_id)
         return g.doc_statuses[study_id]
 
+
     @staticmethod
     def __get_documents_status(study_id):
         """Returns a list of documents related to the study, and any file information

migrations/versions/8f0d445dd297_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: 8f0d445dd297
+Revises: 28752ce0775c
+Create Date: 2022-03-17 16:51:29.873798
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '8f0d445dd297'
+down_revision = '28752ce0775c'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('progress', sa.Integer(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('study', 'progress')
+    # ### end Alembic commands ###

migrations/versions/a345e44ecd27_merge_multiple_heads.py

@@ -0,0 +1,24 @@
+"""merge multiple heads
+
+Revision ID: a345e44ecd27
+Revises: 2b1ec2118bf3, 8f0d445dd297
+Create Date: 2022-03-18 12:40:48.019863
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'a345e44ecd27'
+down_revision = ('2b1ec2118bf3', '8f0d445dd297')
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass