import json import os from datetime import datetime from uuid import UUID from xml.etree import ElementTree from pandas import ExcelFile from crc import session from crc.api.common import ApiError from crc.models.file import FileType, FileDataModel, FileModel from crc.models.workflow import WorkflowSpecModel from crc.services.workflow_processor import WorkflowProcessor import hashlib class FileService(object): """Provides consistent management and rules for storing, retrieving and processing files.""" IRB_PRO_CATEGORIES_FILE = "irb_documents.xlsx" @staticmethod def add_workflow_spec_file(workflow_spec: WorkflowSpecModel, name, content_type, binary_data, primary=False, is_status=False): """Create a new file and associate it with a workflow spec.""" file_model = FileModel( workflow_spec_id=workflow_spec.id, name=name, primary=primary, is_status=is_status ) if primary: bpmn: ElementTree.Element = ElementTree.fromstring(binary_data) workflow_spec.primary_process_id = WorkflowProcessor.get_process_id(bpmn) print("Locating Process Id for " + name + " " + workflow_spec.primary_process_id) return FileService.update_file(file_model, binary_data, content_type) @staticmethod def add_form_field_file(study_id, workflow_id, task_id, form_field_key, name, content_type, binary_data): """Create a new file and associate it with a user task form field within a workflow. Please note that the form_field_key MUST be a known file in the irb_documents.xslx reference document.""" if not FileService.irb_document_reference_exists(form_field_key): raise ApiError("invalid_form_field_key", "When uploading files, the form field id must match a known document in the " "irb_docunents.xslx reference file. This code is not found in that file '%s'" % form_field_key) file_model = FileModel( study_id=study_id, workflow_id=workflow_id, task_id=task_id, name=name, form_field_key=form_field_key, irb_doc_code=form_field_key ) return FileService.update_file(file_model, binary_data, content_type) @staticmethod def irb_document_reference_exists(code): data_model = FileService.get_reference_file_data(FileService.IRB_PRO_CATEGORIES_FILE) xls = ExcelFile(data_model.data) df = xls.parse(xls.sheet_names[0]) return code in df['Code'].values @staticmethod def get_file_reference_dictionary(): """Loads up the xsl file that contains the IRB Pro Categories and converts it to a Panda's data frame for processing.""" data_model = FileService.get_reference_file_data(FileService.IRB_PRO_CATEGORIES_FILE) xls = ExcelFile(data_model.data) df = xls.parse(xls.sheet_names[0]) df['Id'] = df['Id'].fillna(0) df = df.astype({'Id': 'Int64'}) df = df.fillna('') df = df.applymap(str) df = df.set_index('Code') # IF we need to convert the column names to something more sensible. # df.columns = [snakeCase(x) for x in df.columns] return json.loads(df.to_json(orient='index')) # # Pandas is lovely, but weird. Here we drop records without an Id, and convert it to an integer. # df = df.drop_duplicates(subset='Id').astype({'Id': 'Int64'}) # Now we index on the ID column and convert to a dictionary, where the key is the id, and the value # is a dictionary with all the remaining data in it. It's kinda pretty really. # all_dict = df.set_index('Id').to_dict('index') @staticmethod def add_task_file(study_id, workflow_id, task_id, name, content_type, binary_data, irb_doc_code=None): """Create a new file and associate it with an executing task within a workflow.""" file_model = FileModel( study_id=study_id, workflow_id=workflow_id, task_id=task_id, name=name, irb_doc_code=irb_doc_code ) return FileService.update_file(file_model, binary_data, content_type) @staticmethod def add_reference_file(name, content_type, binary_data): """Create a file with the given name, but not associated with a spec or workflow. Only one file with the given reference name can exist.""" file_model = session.query(FileModel). \ filter(FileModel.is_reference == True). \ filter(FileModel.name == name).first() if not file_model: file_model = FileModel( name=name, is_reference=True ) return FileService.update_file(file_model, binary_data, content_type) @staticmethod def get_extension(file_name): basename, file_extension = os.path.splitext(file_name) return file_extension.lower().strip()[1:] @staticmethod def update_file(file_model, binary_data, content_type): file_data_model = session.query(FileDataModel).\ filter_by(file_model_id=file_model.id, version=file_model.latest_version ).with_for_update().first() md5_checksum = UUID(hashlib.md5(binary_data).hexdigest()) if(file_data_model is not None and md5_checksum == file_data_model.md5_hash): # This file does not need to be updated, it's the same file. return file_model # Verify the extension file_extension = FileService.get_extension(file_model.name) if file_extension not in FileType._member_names_: raise ApiError('unknown_extension', 'The file you provided does not have an accepted extension:' + file_extension, status_code=404) else: file_model.type = FileType[file_extension] file_model.content_type = content_type if file_data_model is None: version = 1 else: version = file_data_model.version + 1 file_model.latest_version = version file_data_model = FileDataModel(data=binary_data, file_model=file_model, version=version, md5_hash=md5_checksum, last_updated=datetime.now()) session.add_all([file_model, file_data_model]) session.commit() session.flush() # Assure the id is set on the model before returning it. return file_model @staticmethod def get_files(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None, name=None, is_reference=False, irb_doc_code=None): query = session.query(FileModel).filter_by(is_reference=is_reference) if workflow_spec_id: query = query.filter_by(workflow_spec_id=workflow_spec_id) if study_id: query = query.filter_by(study_id=study_id) if workflow_id: query = query.filter_by(workflow_id=workflow_id) if task_id: query = query.filter_by(task_id=str(task_id)) if form_field_key: query = query.filter_by(form_field_key=form_field_key) if name: query = query.filter_by(name=form_field_key) if irb_doc_code: query = query.filter_by(irb_doc_code=irb_doc_code) results = query.all() return results @staticmethod def get_file_data(file_id, file_model=None): """Returns the file_data that is associated with the file model id, if an actual file_model is provided, uses that rather than looking it up again.""" if file_model is None: file_model = session.query(FileModel).filter(FileModel.id == file_id).first() return session.query(FileDataModel) \ .filter(FileDataModel.file_model_id == file_id) \ .filter(FileDataModel.version == file_model.latest_version) \ .first() @staticmethod def get_reference_file_data(file_name): file_model = session.query(FileModel). \ filter(FileModel.is_reference == True). \ filter(FileModel.name == file_name).first() if not file_model: raise ApiError("file_not_found", "There is no reference file with the name '%s'" % file_name) return FileService.get_file_data(file_model.id, file_model) @staticmethod def get_workflow_file_data(workflow, file_name): """Given a SPIFF Workflow Model, tracks down a file with the given name in the datbase and returns it's data""" workflow_spec_model = FileService.__find_spec_model_in_db(workflow) study_id = workflow.data[WorkflowProcessor.STUDY_ID_KEY] if workflow_spec_model is None: raise ApiError(code="workflow_model_error", message="Something is wrong. I can't find the workflow you are using.") file_data_model = session.query(FileDataModel) \ .join(FileModel) \ .filter(FileModel.name == file_name) \ .filter(FileModel.workflow_spec_id == workflow_spec_model.id).first() if file_data_model is None: raise ApiError(code="file_missing", message="Can not find a file called '%s' within workflow specification '%s'" % (file_name, workflow_spec_model.id)) return file_data_model @staticmethod def __find_spec_model_in_db(workflow): """ Search for the workflow """ # When the workflow spec model is created, we record the primary process id, # then we can look it up. As there is the potential for sub-workflows, we # may need to travel up to locate the primary process. spec = workflow.spec workflow_model = session.query(WorkflowSpecModel). \ filter(WorkflowSpecModel.primary_process_id == spec.name).first() if workflow_model is None and workflow != workflow.outer_workflow: return FileService.__find_spec_model_in_db(workflow.outer_workflow) return workflow_model