Add file_data_get and file_data_set functions that can be accessed in a bpmn script function

Fixes #299

crc/models/data_store.py

@@ -16,6 +16,7 @@ class DataStoreModel(db.Model):
     task_id = db.Column(db.String)
     spec_id = db.Column(db.String)
     user_id = db.Column(db.String, nullable=True)
+    file_id = db.Column(db.Integer, db.ForeignKey('file.id'), nullable=True)
     value = db.Column(db.String)
 
 

crc/models/file.py

@@ -6,7 +6,8 @@ from marshmallow_enum import EnumField
 from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 from sqlalchemy import func, Index
 from sqlalchemy.dialects.postgresql import UUID
-from sqlalchemy.orm import deferred
+from sqlalchemy.orm import deferred, relationship
+from crc.models.data_store import DataStoreModel # this is needed by the relationship
 
 from crc import db, ma
 
@@ -87,6 +88,7 @@ class FileModel(db.Model):
     # it instead, hide it in the interface.
     is_review = db.Column(db.Boolean, default=False, nullable=True)
     archived = db.Column(db.Boolean, default=False, nullable=False)
+    tags = relationship("DataStoreModel", cascade="all,delete", backref="file")
 
 class File(object):
     @classmethod

crc/scripts/data_store_base.py

@@ -38,14 +38,29 @@ class DataStoreBase(object):
                            message=f"The {script_name} script takes two arguments, starting with the key and a " 
                                    "value for the key")
 
-    def get_prev_value(self, study_id, user_id, key):
+    def get_prev_value(self, study_id, user_id, key, file_id):
-        study = session.query(DataStoreModel).filter_by(study_id=study_id, user_id=user_id, key=key).first()
+        study = session.query(DataStoreModel).filter_by(study_id=study_id,
+                                                        user_id=user_id,
+                                                        file_id=file_id,
+                                                        key=key).first()
         return study
 
-    def set_data_common(self, task_id, study_id, user_id, workflow_id, workflow_spec_id, script_name, *args, **kwargs):
+    def set_data_common(self,
+                        task_id,
+                        study_id,
+                        user_id,
+                        workflow_id,
+                        workflow_spec_id,
+                        script_name,
+                        file_id,
+                        *args,
+                        **kwargs):
 
         self.check_args_2(args, script_name=script_name)
-        study = self.get_prev_value(study_id=study_id, user_id=user_id, key=args[0])
+        study = self.get_prev_value(study_id=study_id,
+                                    user_id=user_id,
+                                    file_id=file_id,
+                                    key=args[0])
         if workflow_spec_id is None and workflow_id is not None:
             workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
             workflow_spec_id = workflow.workflow_spec_id
@@ -57,6 +72,7 @@ class DataStoreBase(object):
                                    study_id=study_id,
                                    task_id=task_id,
                                    user_id=user_id,  # Make this available to any User
+                                   file_id=file_id,
                                    workflow_id=workflow_id,
                                    spec_id=workflow_spec_id)
         study.value = args[1]
@@ -68,14 +84,20 @@ class DataStoreBase(object):
                 'old_value': prev_value,
                 'overwritten': overwritten}
 
-    def get_data_common(self, study_id, user_id, script_name, *args):
+    def get_data_common(self, study_id, user_id, script_name, file_id=None, *args):
         self.check_args(args, 2, script_name)
-        study = session.query(DataStoreModel).filter_by(study_id=study_id, user_id=user_id, key=args[0]).first()
+        study = session.query(DataStoreModel).filter_by(study_id=study_id,
+                                                        user_id=user_id,
+                                                        file_id=file_id,
+                                                        key=args[
+            0]).first()
         if study:
             return study.value
         else:
             return args[1]
 
-    def get_multi_common(self, study_id, user_id):
+    def get_multi_common(self, study_id, user_id, file_id=None):
-        study = session.query(DataStoreModel).filter_by(study_id=study_id, user_id=user_id)
+        study = session.query(DataStoreModel).filter_by(study_id=study_id,
+                                                        user_id=user_id,
+                                                        file_id=file_id)
         return study

crc/scripts/study_data_get.py

@@ -13,5 +13,6 @@ class StudyDataGet(Script,DataStoreBase):
         return self.get_data_common(study_id,
                                     None,
                                     'study_data_get',
+                                    None,
                                     *args)
 

crc/scripts/user_data_get.py

@@ -15,4 +15,5 @@ class UserDataGet(Script, DataStoreBase):
         return self.get_data_common(None,
                                     g.user.uid,
                                     'user_data_get',
+                                    None,
                                     *args)