Add in api changes

crc/api.yml

@@ -1026,6 +1026,148 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/Approval"
+  /datastore/study/get:
+    parameters:
+      - name: key
+        in: query
+        required: true
+        description: The key to lookup.
+        schema:
+          type: string
+          format: string
+      - name: default
+        in: query
+        required: false
+        description: Default Value if key doesn't exist.
+        schema:
+          type: string
+          format: string
+      - name: study_id
+        in: query
+        required: true
+        description: The study id we are concerned with .
+        schema:
+          type: integer
+          format: int32
+    get:
+      operationId: crc.api.data_store.study_data_get
+      summary: Provides a single study
+      tags:
+        - DataStore
+      responses:
+        '200':
+          description: A value from the data store, or a default if provided, or None if not found.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Study"
+  /datastore/study/set:
+    parameters:
+      - name: key
+        in: query
+        required: true
+        description: The key to lookup.
+        schema:
+          type: string
+          format: string
+      - name: value
+        in: query
+        required: true
+        description: Default Value if key doesn't exist.
+        schema:
+          type: string
+          format: string
+      - name: study_id
+        in: query
+        required: true
+        description: The study id we are concerned with .
+        schema:
+          type: integer
+          format: int32
+    get:
+      operationId: crc.api.data_store.study_data_set
+      summary: Provides a single study
+      tags:
+        - DataStore
+      responses:
+        '200':
+          description: Sets a value in the data store for a study.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Study"
+  /datastore/user/get:
+    parameters:
+      - name: key
+        in: query
+        required: true
+        description: The key to lookup.
+        schema:
+          type: string
+          format: string
+      - name: default
+        in: query
+        required: false
+        description: Default Value if key doesn't exist.
+        schema:
+          type: string
+          format: string
+      - name: user_id
+        in: query
+        required: true
+        description: The study id we are concerned with .
+        schema:
+          type: string
+          format: string
+    get:
+      operationId: crc.api.data_store.user_data_get
+      summary: Provides a single study
+      tags:
+        - DataStore
+      responses:
+        '200':
+          description: A value from the data store, or a default if provided, or None if not found.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Study"
+  /datastore/user/set:
+    parameters:
+      - name: key
+        in: query
+        required: true
+        description: The key to lookup.
+        schema:
+          type: string
+          format: string
+      - name: value
+        in: query
+        required: true
+        description: Default Value if key doesn't exist.
+        schema:
+          type: string
+          format: string
+      - name: user_id
+        in: query
+        required: true
+        description: The user id we are concerned with .
+        schema:
+          type: string
+          format: string
+    get:
+      operationId: crc.api.data_store.user_data_set
+      summary: Provides a single study
+      tags:
+        - DataStore
+      responses:
+        '200':
+          description: Sets a value in the data store for a study.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Study"
+
+
 components:
   securitySchemes:
     jwt:
@@ -1495,4 +1637,3 @@ components:
           type: number
           format: integer
           example: 5
-

crc/api/data_store.py

@@ -0,0 +1,73 @@
+from datetime import datetime
+
+from flask import g
+from sqlalchemy.exc import IntegrityError
+import json
+from crc import session
+from crc.scripts.script import DataStoreBase
+from crc.api.common import ApiError, ApiErrorSchema
+from crc.models.data_store import DataStoreModel
+
+
+def study_data_set(study_id,key,value):
+    """Set a study data value in the data_store, mimic the script endpoint"""
+    if study_id is None:
+        raise ApiError('unknown_study', 'Please provide a valid Study ID.')
+
+    if key is None:
+        raise ApiError('invalid_key', 'Please provide a valid key')
+    dsb = DataStoreBase()
+    retval=dsb.set_data_common('api',study_id,None,None,None,'api_study_data_set',key,value)
+    json_value = json.dumps(retval, ensure_ascii=False, indent=2)
+    return json_value
+
+def study_data_get(study_id,key,default=None):
+    """Set a study data value in the data_store, mimic the script endpoint"""
+    if study_id is None:
+        raise ApiError('unknown_study', 'Please provide a valid Study ID.')
+
+    if key is None:
+        raise ApiError('invalid_key', 'Please provide a valid key')
+    dsb = DataStoreBase()
+    retval=dsb.get_data_common(study_id,None,'api_study_data_get',key,default)
+    json_value = json.dumps(retval, ensure_ascii=False, indent=2)
+    return json_value
+
+
+def user_data_set(user_id,key,value):
+    """Set a user data value in the data_store, mimic the script endpoint"""
+    if user_id is None:
+        raise ApiError('unknown_study', 'Please provide a valid UserID.')
+
+    if key is None:
+        raise ApiError('invalid_key', 'Please provide a valid key')
+    dsb = DataStoreBase()
+
+    retval=dsb.set_data_common('api',
+                               None,
+                               user_id,
+                               None,
+                               None,
+                               'api_user_data_set',
+                               key,value)
+
+    json_value = json.dumps(retval, ensure_ascii=False, indent=2)
+    return json_value
+
+
+def user_data_get(user_id,key,default=None):
+    """Set a user data value in the data_store, mimic the script endpoint"""
+    if user_id is None:
+        raise ApiError('unknown_study', 'Please provide a valid UserID.')
+
+    if key is None:
+        raise ApiError('invalid_key', 'Please provide a valid key')
+    dsb = DataStoreBase()
+    retval=dsb.get_data_common(None,
+                               user_id,
+                               'api_user_data_get',
+                               key,default)
+
+    json_value = json.dumps(retval, ensure_ascii=False, indent=2)
+    return json_value
+

crc/scripts/script.py

@@ -144,25 +144,30 @@ class DataStoreBase():
         study = session.query(DataStoreModel).filter_by(study_id=study_id,user_id=user_id,key=key).first()
         return study
 
-    def set_data_common(self, task, study_id, user_id, workflow_id, script_name, *args, **kwargs):
+    def set_data_common(self, task_id, study_id, user_id, workflow_id, workflow_spec_id, script_name, *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])
-        workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
+        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
         if study is not None:
-            prev_value = study.key
+            prev_value = study.value
         else:
             prev_value = None
             study = DataStoreModel(key=args[0],value=args[1],
                                    study_id=study_id,
-                                   task_id=task.id,
+                                   task_id=task_id,
                                    user_id=user_id,             # Make this available to any User
                                    workflow_id= workflow_id,
-                                   spec_id=workflow.workflow_spec_id)
-
+                                   spec_id=workflow_spec_id)
+        study.value = args[1]
         overwritten = self.overwritten(study.value,prev_value)
         session.add(study)
-        return (study.value, prev_value, overwritten)
+        session.commit()
+        return {'new_value':study.value,
+                'old_value':prev_value,
+                'overwritten':overwritten}
 
 
     def get_data_common(self, study_id, user_id, script_name, *args):

crc/scripts/study_data_set.py

@@ -19,10 +19,11 @@ class StudyDataSet(Script,DataStoreBase):
 
 
     def do_task(self, task, study_id, workflow_id, *args, **kwargs):
-        return self.set_data_common(task,
+        return self.set_data_common(task.id,
                                     study_id,
                                     None,
                                     workflow_id,
+                                    None,
                                     'study_data_set',
                                     *args,
                                     **kwargs)

crc/scripts/user_data_set.py

@@ -21,10 +21,11 @@ class UserDataSet(Script,DataStoreBase):
 
 
     def do_task(self, task, study_id, workflow_id, *args, **kwargs):
-        return self.set_data_common(task,
+        return self.set_data_common(task.id,
                                     None,
                                     g.user.uid,
                                     workflow_id,
+                                    None,
                                     'user_data_set',
                                     *args,
                                     **kwargs)

tests/study/test_study_data_store_script.py

@@ -17,6 +17,7 @@ class TestSudySponsorsScript(BaseTest):
 
 
     def test_study_sponsors_script_validation(self):
+        flask.g.user = UserModel(uid='dhf8r')
         self.load_example_data() # study_info script complains if irb_documents.xls is not loaded
                                  # during the validate phase I'm going to assume that we will never
                                  # have a case where irb_documents.xls is not loaded ??