From 9ea1399578ca6445233c8903cb46fb3282ab655e Mon Sep 17 00:00:00 2001
From: mike cullerton <michaelc@cullerton.com>
Date: Thu, 20 Jan 2022 09:54:22 -0500
Subject: [PATCH] get_files needs to have workflow_spec_id

---
 crc/api.yml                  |  6 ++++++
 crc/api/file.py              | 13 +++++++------
 crc/services/file_service.py | 34 ++++++++++++++++++++++++----------
 3 files changed, 37 insertions(+), 16 deletions(-)

diff --git a/crc/api.yml b/crc/api.yml
index 6a4ff322..5bd1be74 100755
--- a/crc/api.yml
+++ b/crc/api.yml
@@ -802,6 +802,12 @@ paths:
 
   /file:
     parameters:
+      - name: workflow_spec_id
+        in: query
+        required: false
+        description: The unique id of a workflow specification
+        schema:
+          type: string
       - name: workflow_id
         in: query
         required: false
diff --git a/crc/api/file.py b/crc/api/file.py
index ca438810..13ab8b50 100644
--- a/crc/api/file.py
+++ b/crc/api/file.py
@@ -28,21 +28,22 @@ def to_file_api(file_model):
                             DocumentService.get_dictionary())
 
 
-def get_files(workflow_id=None, form_field_key=None,study_id=None):
-    if workflow_id is None:
+def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None,study_id=None):
+    if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key,study_id]):
         raise ApiError('missing_parameter',
-                       'Please specify a workflow_id with an optional form_field_key')
+                       'Please specify either a workflow_spec_id or a '
+                       'workflow_id with an optional form_field_key')
 
     if study_id is not None:
         file_models = FileService.get_files_for_study(study_id=study_id, irb_doc_code=form_field_key)
     else:
-        file_models = FileService.get_files(workflow_id=workflow_id,
-                                            irb_doc_code=form_field_key)
+        file_models = FileService.get_files(workflow_spec_id=workflow_spec_id,
+                                        workflow_id=workflow_id,
+                                        irb_doc_code=form_field_key)
 
     files = (to_file_api(model) for model in file_models)
     return FileSchema(many=True).dump(files)
 
-
 def get_spec_files(workflow_spec_id, include_libraries=False):
     if workflow_spec_id is None:
         raise ApiError(code='missing_spec_id',
diff --git a/crc/services/file_service.py b/crc/services/file_service.py
index dca5cf2f..0b4649eb 100644
--- a/crc/services/file_service.py
+++ b/crc/services/file_service.py
@@ -16,7 +16,7 @@ from crc import session, app
 from crc.api.common import ApiError
 from crc.models.data_store import DataStoreModel
 from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
-from crc.models.workflow import WorkflowModel
+from crc.models.workflow import WorkflowModel, WorkflowLibraryModel
 from crc.services.cache_service import cache
 from crc.services.user_service import UserService
 import re
@@ -163,21 +163,35 @@ class FileService(object):
         return query.all()
 
     @staticmethod
-    def get_files(workflow_id=None, name=None, irb_doc_code=None):
-        if workflow_id is not None:
-            query = session.query(FileModel).filter_by(workflow_id=workflow_id)
+    def get_files(workflow_spec_id=None, workflow_id=None,
+                  name=None, is_reference=False, irb_doc_code=None, include_libraries=False):
+        query = session.query(FileModel).filter_by(is_reference=is_reference)
+        if workflow_spec_id:
+            if include_libraries:
+                libraries = session.query(WorkflowLibraryModel).filter(
+                   WorkflowLibraryModel.workflow_spec_id==workflow_spec_id).all()
+                library_workflow_specs = [x.library_spec_id for x in libraries]
+                library_workflow_specs.append(workflow_spec_id)
+                query = query.filter(FileModel.workflow_spec_id.in_(library_workflow_specs))
+            else:
+                query = query.filter(FileModel.workflow_spec_id == workflow_spec_id)
+
+        elif workflow_id:
+            query = query.filter_by(workflow_id=workflow_id)
             if irb_doc_code:
                 query = query.filter_by(irb_doc_code=irb_doc_code)
+        elif is_reference:
+            query = query.filter_by(is_reference=True)
 
-            if name:
-                query = query.filter_by(name=name)
+        if name:
+            query = query.filter_by(name=name)
 
-            query = query.filter(FileModel.archived == False)
-            query = query.order_by(FileModel.id)
+        query = query.filter(FileModel.archived == False)
 
-            results = query.all()
-            return results
+        query = query.order_by(FileModel.id)
 
+        results = query.all()
+        return results
 
     @staticmethod
     def get_workflow_data_files(workflow_id=None):