New script to created a zipped file of irb_documents for use as an email attachment.

The script accepts a list of file_ids, and generates a list of documents from these ids.
The documents are stored in a directory structure generated from the categories in the irb_documents spreadsheet

crc/scripts/get_zipped_files.py

@@ -0,0 +1,58 @@
+from crc import session
+from crc.api.common import ApiError
+from crc.models.file import FileModel, FileDataModel
+from crc.scripts.script import Script
+from crc.services.file_service import FileService
+from crc.services.study_service import StudyService
+
+import os
+import zipfile
+
+
+class GetZippedFiles(Script):
+
+    """This script creates a zip document from a list of file ids"""
+
+    def get_description(self):
+        """Creates a zip file from a list of file_ids.
+           This is meant to use as an attachment to an email message"""
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        if 'file_ids' in kwargs.keys():
+            return True
+        return False
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+
+        doc_info = StudyService().get_documents_status(study_id)
+        if 'filename' in kwargs.keys():
+            zip_filename = kwargs['filename']
+        else:
+            zip_filename = 'attachments.zip'
+
+        if 'file_ids' in kwargs.keys():
+            file_ids = kwargs['file_ids']
+            files = session.query(FileModel).filter(FileModel.id.in_(file_ids)).all()
+            if files:
+                with zipfile.ZipFile(zip_filename, mode='x', compression=zipfile.ZIP_DEFLATED) as zfw:
+                    for file in files:
+                        file_doc_info = doc_info[file.irb_doc_code]
+                        file_path = '/'
+                        if file_doc_info['category1'] != '':
+                            file_path = os.path.join(file_path, file_doc_info['category1'])
+                            if file_doc_info['category2'] != '':
+                                file_path = os.path.join(file_path, file_doc_info['category2'])
+                                if file_doc_info['category3'] != '':
+                                    file_path = os.path.join(file_path, file_doc_info['category3'])
+
+                        file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == file.id).first()
+                        zfw.writestr(os.path.join(file_path, file.name), file_data.data)
+
+                with open(zip_filename, mode='rb') as handle:
+                    file_model = FileService().add_workflow_file(workflow_id, None, zip_filename, 'application/zip', handle.read())
+                os.remove(zip_filename)
+
+        else:
+            raise ApiError(code='missing_file_ids',
+                           message='You must include a list of file_ids.')
+        return file_model