Refactoring Reference files to use the lookup table, rather than parsing the results directly out of the spreadsheet, or attempting to cache them.
Adding a DocumentService to clean up the FileService, and get Documents well seperated, as it seems likely be pulled out or seperated in the future, there is now a Documents api file as well, for the same reason. Some other minor changes are just fixing white space to assure our code is linting correctly. I removed _create_study_workflow_approvals from the base test, as we don't use approvals like this anymore.
This commit is contained in:
Dan
parent
fafa79a07d
commit
1b1a994360
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@ -55,7 +55,7 @@ def process_waiting_tasks():
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with app.app_context():
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WorkflowService.do_waiting()
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scheduler.add_job(process_waiting_tasks,'interval',minutes=5)
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scheduler.add_job(process_waiting_tasks,'interval',minutes=1)
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scheduler.start()
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@ -82,7 +82,7 @@ paths:
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schema :
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type : integer
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get:
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operationId: crc.api.file.get_document_directory
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operationId: crc.api.document.get_document_directory
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summary: Returns a directory of all files for study in a nested structure
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tags:
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- Document Categories
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@ -0,0 +1,18 @@
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from crc.models.api_models import DocumentDirectorySchema
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from crc.models.file import File
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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from crc.services.lookup_service import LookupService
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def get_document_directory(study_id, workflow_id=None):
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"""
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return a nested list of files arranged according to the category hierarchy
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defined in the doc dictionary
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"""
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file_models = FileService.get_files_for_study(study_id=study_id)
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doc_dict = DocumentService.get_dictionary()
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files = (File.from_models(model, FileService.get_file_data(model.id), doc_dict) for model in file_models)
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directory = DocumentService.get_directory(doc_dict, files, workflow_id)
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return DocumentDirectorySchema(many=True).dump(directory)
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@ -7,71 +7,15 @@ from flask import send_file
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from crc import session
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from crc.api.common import ApiError
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from crc.api.user import verify_token
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from crc.models.api_models import DocumentDirectory, DocumentDirectorySchema
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from crc.models.file import FileSchema, FileModel, File, FileModelSchema, FileDataModel, FileType
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from crc.models.workflow import WorkflowSpecModel
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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def ensure_exists(output, categories, expanded):
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"""
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This is a recursive function, it expects a list of
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levels with a file object at the end (kinda like duck,duck,duck,goose)
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for each level, it makes sure that level is already in the structure and if it is not
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it will add it
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function terminates upon getting an entry that is a file object ( or really anything but string)
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"""
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current_item = categories[0]
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found = False
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if isinstance(current_item, str):
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for item in output:
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if item.level == current_item:
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found = True
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item.filecount = item.filecount + 1
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item.expanded = expanded | item.expanded
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ensure_exists(item.children, categories[1:], expanded)
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if not found:
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new_level = DocumentDirectory(level=current_item)
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new_level.filecount = 1
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new_level.expanded = expanded
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output.append(new_level)
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ensure_exists(new_level.children, categories[1:], expanded)
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else:
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new_level = DocumentDirectory(file=current_item)
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new_level.expanded = expanded
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output.append(new_level)
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def get_document_directory(study_id, workflow_id=None):
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"""
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return a nested list of files arranged according to the category hirearchy
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defined in the doc dictionary
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"""
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output = []
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doc_dict = FileService.get_doc_dictionary()
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file_models = FileService.get_files_for_study(study_id=study_id)
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files = (to_file_api(model) for model in file_models)
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for file in files:
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if file.irb_doc_code in doc_dict:
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doc_code = doc_dict[file.irb_doc_code]
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else:
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doc_code = {'category1': "Unknown", 'category2': '', 'category3': ''}
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if workflow_id:
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expand = file.workflow_id == int(workflow_id)
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else:
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expand = False
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print(expand)
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categories = [x for x in [doc_code['category1'],doc_code['category2'],doc_code['category3'],file] if x != '']
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ensure_exists(output, categories, expanded=expand)
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return DocumentDirectorySchema(many=True).dump(output)
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def to_file_api(file_model):
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"""Converts a FileModel object to something we can return via the api"""
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return File.from_models(file_model, FileService.get_file_data(file_model.id),
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FileService.get_doc_dictionary())
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DocumentService.get_dictionary())
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def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None,study_id=None):
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@ -1,15 +1,14 @@
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import enum
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from typing import cast
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from marshmallow import INCLUDE, EXCLUDE, fields, Schema
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from marshmallow import INCLUDE, EXCLUDE, Schema
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from marshmallow_enum import EnumField
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from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
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from sqlalchemy import func, Index
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from sqlalchemy.dialects.postgresql import UUID
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from sqlalchemy.orm import deferred, relationship
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from crc.models.data_store import DataStoreModel # this is needed by the relationship
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from crc import db, ma
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from crc.models.data_store import DataStoreModel
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class FileType(enum.Enum):
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@ -43,7 +42,7 @@ CONTENT_TYPES = {
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"docx": "application/vnd.openxmlformats-officedocument.wordprocessingml.document",
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"gif": "image/gif",
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"jpg": "image/jpeg",
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"md" : "text/plain",
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"md": "text/plain",
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"pdf": "application/pdf",
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"png": "image/png",
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"ppt": "application/vnd.ms-powerpoint",
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@ -71,7 +70,6 @@ class FileDataModel(db.Model):
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file_model = db.relationship("FileModel", foreign_keys=[file_model_id])
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class FileModel(db.Model):
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__tablename__ = 'file'
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id = db.Column(db.Integer, primary_key=True)
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@ -79,18 +77,19 @@ class FileModel(db.Model):
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type = db.Column(db.Enum(FileType))
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is_status = db.Column(db.Boolean)
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content_type = db.Column(db.String)
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is_reference = db.Column(db.Boolean, nullable=False, default=False) # A global reference file.
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primary = db.Column(db.Boolean, nullable=False, default=False) # Is this the primary BPMN in a workflow?
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primary_process_id = db.Column(db.String, nullable=True) # An id in the xml of BPMN documents, critical for primary BPMN.
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is_reference = db.Column(db.Boolean, nullable=False, default=False) # A global reference file.
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primary = db.Column(db.Boolean, nullable=False, default=False) # Is this the primary BPMN in a workflow?
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primary_process_id = db.Column(db.String, nullable=True) # An id in the xml of BPMN documents, for primary BPMN.
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workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
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workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=True)
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irb_doc_code = db.Column(db.String, nullable=True) # Code reference to the irb_documents.xlsx reference file.
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irb_doc_code = db.Column(db.String, nullable=True) # Code reference to the irb_documents.xlsx reference file.
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# A request was made to delete the file, but we can't because there are
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# active approvals or running workflows that depend on it. So we archive
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# it instead, hide it in the interface.
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is_review = db.Column(db.Boolean, default=False, nullable=True)
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archived = db.Column(db.Boolean, default=False, nullable=False)
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data_stores = relationship("DataStoreModel", cascade="all,delete", backref="file")
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data_stores = relationship(DataStoreModel, cascade="all,delete", backref="file")
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class File(object):
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@classmethod
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@ -107,7 +106,7 @@ class File(object):
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instance.workflow_id = model.workflow_id
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instance.irb_doc_code = model.irb_doc_code
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instance.type = model.type
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if model.irb_doc_code and model.irb_doc_code in doc_dictionary:
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if model.irb_doc_code and model.irb_doc_code in doc_dictionary:
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instance.document = doc_dictionary[model.irb_doc_code]
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else:
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instance.document = {}
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@ -147,7 +146,6 @@ class FileSchema(Schema):
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type = EnumField(FileType)
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class LookupFileModel(db.Model):
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"""Gives us a quick way to tell what kind of lookup is set on a form field.
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Connected to the file data model, so that if a new version of the same file is
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@ -158,8 +156,10 @@ class LookupFileModel(db.Model):
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task_spec_id = db.Column(db.String)
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field_id = db.Column(db.String)
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is_ldap = db.Column(db.Boolean) # Allows us to run an ldap query instead of a db lookup.
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is_reference = db.Column(db.Boolean) # For lookup models that are globally referenced.
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file_data_model_id = db.Column(db.Integer, db.ForeignKey('file_data.id'))
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dependencies = db.relationship("LookupDataModel", lazy="select", backref="lookup_file_model", cascade="all, delete, delete-orphan")
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dependencies = db.relationship("LookupDataModel", lazy="select", backref="lookup_file_model",
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cascade="all, delete, delete-orphan")
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class LookupDataModel(db.Model):
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@ -169,7 +169,7 @@ class LookupDataModel(db.Model):
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value = db.Column(db.String)
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label = db.Column(db.String)
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# In the future, we might allow adding an additional "search" column if we want to search things not in label.
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data = db.Column(db.JSON) # all data for the row is stored in a json structure here, but not searched presently.
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data = db.Column(db.JSON) # all data for the row is stored in a json structure here, but not searched presently.
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# Assure there is a searchable index on the label column, so we can get fast results back.
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# query with:
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@ -192,7 +192,7 @@ class LookupDataSchema(SQLAlchemyAutoSchema):
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load_instance = True
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include_relationships = False
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include_fk = False # Includes foreign keys
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exclude = ['id'] # Do not include the id field, it should never be used via the API.
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exclude = ['id'] # Do not include the id field, it should never be used via the API.
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class SimpleFileSchema(ma.Schema):
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@ -2,6 +2,7 @@ from crc import session
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from crc.api.common import ApiError
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from crc.models.file import FileModel
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from crc.scripts.script import Script
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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@ -9,7 +10,7 @@ class DeleteFile(Script):
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@staticmethod
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def process_document_deletion(doc_code, workflow_id, task):
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if FileService.is_allowed_document(doc_code):
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if DocumentService.is_allowed_document(doc_code):
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result = session.query(FileModel).filter(
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FileModel.workflow_id == workflow_id, FileModel.irb_doc_code == doc_code).all()
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if isinstance(result, list) and len(result) > 0 and isinstance(result[0], FileModel):
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@ -3,6 +3,7 @@ from flask import g
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from crc.api.common import ApiError
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from crc.services.data_store_service import DataStoreBase
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from crc.scripts.script import Script
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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@ -17,17 +18,22 @@ class FileDataSet(Script, DataStoreBase):
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del(kwargs['file_id'])
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return True
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def validate_kw_args(self,**kwargs):
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if kwargs.get('key',None) is None:
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def validate_kw_args(self, **kwargs):
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if kwargs.get('key', None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'key'")
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message=f"The 'file_data_get' script requires a keyword argument of 'key'")
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if kwargs.get('file_id', None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'file_id'")
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if kwargs.get('value', None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'value'")
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if kwargs.get('file_id',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'file_id'")
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if kwargs.get('value',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'value'")
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if kwargs['key'] == 'irb_code' and not DocumentService.is_allowed_document(kwargs.get('value')):
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raise ApiError("invalid_form_field_key",
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"When setting an irb_code, the form field id must match a known document in the "
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"irb_docunents.xslx reference file. This code is not found in that file '%s'" %
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kwargs.get('value'))
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return True
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@ -10,6 +10,7 @@ from crc.models.protocol_builder import ProtocolBuilderInvestigatorType
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from crc.models.study import StudyModel, StudySchema
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from crc.api import workflow as workflow_api
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from crc.scripts.script import Script
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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from crc.services.protocol_builder import ProtocolBuilderService
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from crc.services.study_service import StudyService
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@ -168,8 +169,8 @@ Please note this is just a few examples, ALL known document types are returned i
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"""For validation only, pretend no results come back from pb"""
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self.check_args(args, 2)
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# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
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FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
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FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
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FileService.get_reference_file_data(DocumentService.DOCUMENT_LIST)
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FileService.get_reference_file_data(StudyService.INVESTIGATOR_LIST)
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# we call the real do_task so we can
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# seed workflow validations with settings from studies in PB Mock
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# in order to test multiple paths thru the workflow
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@ -0,0 +1,92 @@
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from crc.api.common import ApiError
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from crc.models.api_models import DocumentDirectory
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from crc.services.file_service import FileService
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from crc.services.lookup_service import LookupService
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class DocumentService(object):
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DOCUMENT_LIST = "irb_documents.xlsx"
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@staticmethod
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def is_allowed_document(code):
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doc_dict = DocumentService.get_dictionary()
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return code in doc_dict
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@staticmethod
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def verify_doc_dictionary(dd):
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"""
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We are currently getting structured information from an XLS file, if someone accidentally
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changes a header we will have problems later, so we will verify we have the headers we need
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here
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"""
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required_fields = ['category1', 'category2', 'category3', 'description']
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# we only need to check the first item, as all of the keys should be the same
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key = list(dd.keys())[0]
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for field in required_fields:
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if field not in dd[key].keys():
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raise ApiError(code="Invalid document list %s" % DocumentService.DOCUMENT_LIST,
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message='Please check the headers in %s' % DocumentService.DOCUMENT_LIST)
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@staticmethod
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def get_dictionary():
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"""Returns a dictionary of document details keyed on the doc_code."""
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file_data = FileService.get_reference_file_data(DocumentService.DOCUMENT_LIST)
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lookup_model = LookupService.get_lookup_model_for_file_data(file_data, 'code', 'description')
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doc_dict = {}
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for lookup_data in lookup_model.dependencies:
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doc_dict[lookup_data.value] = lookup_data.data
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return doc_dict
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@staticmethod
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def get_directory(doc_dict, files, workflow_id):
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"""Returns a list of directories, hierarchically nested by category, with files at the deepest level.
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Empty directories are not include."""
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directory = []
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if files:
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for file in files:
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if file.irb_doc_code in doc_dict:
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doc_code = doc_dict[file.irb_doc_code]
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else:
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doc_code = {'category1': "Unknown", 'category2': None, 'category3': None}
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if workflow_id:
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expand = file.workflow_id == int(workflow_id)
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else:
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expand = False
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print(expand)
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categories = [x for x in [doc_code['category1'], doc_code['category2'], doc_code['category3'], file] if x]
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DocumentService.ensure_exists(directory, categories, expanded=expand)
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return directory
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@staticmethod
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def ensure_exists(output, categories, expanded):
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"""
|
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This is a recursive function, it expects a list of
|
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levels with a file object at the end (kinda like duck,duck,duck,goose)
|
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|
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for each level, it makes sure that level is already in the structure and if it is not
|
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it will add it
|
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|
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function terminates upon getting an entry that is a file object ( or really anything but string)
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"""
|
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current_item = categories[0]
|
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found = False
|
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if isinstance(current_item, str):
|
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for item in output:
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if item.level == current_item:
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found = True
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item.filecount = item.filecount + 1
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item.expanded = expanded | item.expanded
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DocumentService.ensure_exists(item.children, categories[1:], expanded)
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if not found:
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new_level = DocumentDirectory(level=current_item)
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new_level.filecount = 1
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new_level.expanded = expanded
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output.append(new_level)
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DocumentService.ensure_exists(new_level.children, categories[1:], expanded)
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else:
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print("Found it")
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else:
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new_level = DocumentDirectory(file=current_item)
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new_level.expanded = expanded
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output.append(new_level)
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@ -10,8 +10,6 @@ from lxml import etree
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|
||||
from SpiffWorkflow.bpmn.parser.ValidationException import ValidationException
|
||||
from lxml.etree import XMLSyntaxError
|
||||
from pandas import ExcelFile
|
||||
from pandas._libs.missing import NA
|
||||
from sqlalchemy import desc
|
||||
from sqlalchemy.exc import IntegrityError
|
||||
|
||||
|
|
@ -38,34 +36,6 @@ def camel_to_snake(camel):
|
|||
|
||||
|
||||
class FileService(object):
|
||||
"""Provides consistent management and rules for storing, retrieving and processing files."""
|
||||
DOCUMENT_LIST = "irb_documents.xlsx"
|
||||
INVESTIGATOR_LIST = "investigators.xlsx"
|
||||
|
||||
__doc_dictionary = None
|
||||
|
||||
@staticmethod
|
||||
def verify_doc_dictionary(dd):
|
||||
"""
|
||||
We are currently getting structured information from an XLS file, if someone accidentally
|
||||
changes a header we will have problems later, so we will verify we have the headers we need
|
||||
here
|
||||
"""
|
||||
required_fields = ['category1','category2','category3','description']
|
||||
|
||||
# we only need to check the first item, as all of the keys should be the same
|
||||
key = list(dd.keys())[0]
|
||||
for field in required_fields:
|
||||
if field not in dd[key].keys():
|
||||
raise ApiError(code="Invalid document list %s"%FileService.DOCUMENT_LIST,
|
||||
message='Please check the headers in %s'%FileService.DOCUMENT_LIST)
|
||||
|
||||
@staticmethod
|
||||
def get_doc_dictionary():
|
||||
if not FileService.__doc_dictionary:
|
||||
FileService.__doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
|
||||
FileService.verify_doc_dictionary(FileService.__doc_dictionary)
|
||||
return FileService.__doc_dictionary
|
||||
|
||||
@staticmethod
|
||||
def add_workflow_spec_file(workflow_spec: WorkflowSpecModel,
|
||||
|
|
@ -88,10 +58,7 @@ class FileService(object):
|
|||
|
||||
return FileService.update_file(file_model, binary_data, content_type)
|
||||
|
||||
@staticmethod
|
||||
def is_allowed_document(code):
|
||||
doc_dict = FileService.get_doc_dictionary()
|
||||
return code in doc_dict
|
||||
|
||||
|
||||
@staticmethod
|
||||
@cache
|
||||
|
|
@ -104,12 +71,6 @@ class FileService(object):
|
|||
def update_irb_code(file_id, irb_doc_code):
|
||||
"""Create a new file and associate it with the workflow
|
||||
Please note that the irb_doc_code MUST be a known file in the irb_documents.xslx reference document."""
|
||||
if not FileService.is_allowed_document(irb_doc_code):
|
||||
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'" % irb_doc_code)
|
||||
|
||||
""" """
|
||||
file_model = session.query(FileModel)\
|
||||
.filter(FileModel.id == file_id).first()
|
||||
if file_model is None:
|
||||
|
|
@ -137,28 +98,6 @@ class FileService(object):
|
|||
)
|
||||
return FileService.update_file(file_model, binary_data, content_type)
|
||||
|
||||
@staticmethod
|
||||
def get_reference_data(reference_file_name, index_column, int_columns=[]):
|
||||
""" Opens a reference file (assumes that it is xls file) and returns the data as a
|
||||
dictionary, each row keyed on the given index_column name. If there are columns
|
||||
that should be represented as integers, pass these as an array of int_columns, lest
|
||||
you get '1.0' rather than '1'
|
||||
fixme: This is stupid stupid slow. Place it in the database and just check if it is up to date."""
|
||||
data_model = FileService.get_reference_file_data(reference_file_name)
|
||||
xls = ExcelFile(data_model.data, engine='openpyxl')
|
||||
df = xls.parse(xls.sheet_names[0])
|
||||
df = df.convert_dtypes()
|
||||
df = pd.DataFrame(df).dropna(how='all') # Drop null rows
|
||||
df = pd.DataFrame(df).replace({NA: None}) # replace NA with None.
|
||||
|
||||
for c in int_columns:
|
||||
df[c] = df[c].fillna(0)
|
||||
df = df.astype({c: 'Int64'})
|
||||
df = df.fillna('')
|
||||
df = df.applymap(str)
|
||||
df = df.set_index(index_column)
|
||||
return json.loads(df.to_json(orient='index'))
|
||||
|
||||
@staticmethod
|
||||
def get_workflow_files(workflow_id):
|
||||
"""Returns all the file models associated with a running workflow."""
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ from sqlalchemy.sql.functions import GenericFunction
|
|||
from crc import db
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.api_models import Task
|
||||
from crc.models.file import FileDataModel, LookupFileModel, LookupDataModel
|
||||
from crc.models.file import FileModel, FileDataModel, LookupFileModel, LookupDataModel
|
||||
from crc.models.workflow import WorkflowModel, WorkflowSpecDependencyFile
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
|
|
@ -25,11 +25,14 @@ class TSRank(GenericFunction):
|
|||
|
||||
|
||||
class LookupService(object):
|
||||
"""Provides tools for doing lookups for auto-complete fields.
|
||||
This can currently take two forms:
|
||||
"""Provides tools for doing lookups for auto-complete fields, and rapid access to any
|
||||
uploaded spreadsheets.
|
||||
This can currently take three forms:
|
||||
1) Lookup from spreadsheet data associated with a workflow specification.
|
||||
in which case we store the spreadsheet data in a lookup table with full
|
||||
text indexing enabled, and run searches against that table.
|
||||
2) Lookup from spreadsheet data associated with a specific file. This allows us
|
||||
to get a lookup model for a specific file object, such as a reference file.
|
||||
2) Lookup from LDAP records. In which case we call out to an external service
|
||||
to pull back detailed records and return them.
|
||||
|
||||
|
|
@ -44,6 +47,14 @@ class LookupService(object):
|
|||
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
|
||||
return LookupService.__get_lookup_model(workflow, spiff_task.task_spec.name, field.id)
|
||||
|
||||
@staticmethod
|
||||
def get_lookup_model_for_file_data(file_data: FileDataModel, value_column, label_column):
|
||||
lookup_model = db.session.query(LookupFileModel).filter(LookupFileModel.file_data_model_id == file_data.id).first()
|
||||
if not lookup_model:
|
||||
logging.warning("!!!! Making a very expensive call to update the lookup model.")
|
||||
lookup_model = LookupService.build_lookup_table(file_data, value_column, label_column)
|
||||
return lookup_model
|
||||
|
||||
@staticmethod
|
||||
def __get_lookup_model(workflow, task_spec_id, field_id):
|
||||
lookup_model = db.session.query(LookupFileModel) \
|
||||
|
|
@ -139,7 +150,8 @@ class LookupService(object):
|
|||
return lookup_model
|
||||
|
||||
@staticmethod
|
||||
def build_lookup_table(data_model: FileDataModel, value_column, label_column, workflow_spec_id, task_spec_id, field_id):
|
||||
def build_lookup_table(data_model: FileDataModel, value_column, label_column,
|
||||
workflow_spec_id=None, task_spec_id=None, field_id=None):
|
||||
""" In some cases the lookup table can be very large. This method will add all values to the database
|
||||
in a way that can be searched and returned via an api call - rather than sending the full set of
|
||||
options along with the form. It will only open the file and process the options if something has
|
||||
|
|
|
|||
|
|
@ -22,13 +22,17 @@ from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowM
|
|||
from crc.models.task_event import TaskEventModel, TaskEvent
|
||||
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
|
||||
WorkflowStatus, WorkflowSpecDependencyFile
|
||||
from crc.services.document_service import DocumentService
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
from crc.services.lookup_service import LookupService
|
||||
from crc.services.protocol_builder import ProtocolBuilderService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
|
||||
class StudyService(object):
|
||||
"""Provides common tools for working with a Study"""
|
||||
"""Provides consistent management and rules for storing, retrieving and processing files."""
|
||||
INVESTIGATOR_LIST = "investigators.xlsx"
|
||||
|
||||
@staticmethod
|
||||
def get_studies_for_user(user):
|
||||
|
|
@ -77,7 +81,7 @@ class StudyService(object):
|
|||
workflow_metas = StudyService._get_workflow_metas(study_id)
|
||||
files = FileService.get_files_for_study(study.id)
|
||||
files = (File.from_models(model, FileService.get_file_data(model.id),
|
||||
FileService.get_doc_dictionary()) for model in files)
|
||||
DocumentService.get_dictionary()) for model in files)
|
||||
study.files = list(files)
|
||||
# Calling this line repeatedly is very very slow. It creates the
|
||||
# master spec and runs it. Don't execute this for Abandoned studies, as
|
||||
|
|
@ -265,14 +269,14 @@ class StudyService(object):
|
|||
|
||||
# Loop through all known document types, get the counts for those files,
|
||||
# and use pb_docs to mark those as required.
|
||||
doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
|
||||
doc_dictionary = DocumentService.get_dictionary()
|
||||
|
||||
documents = {}
|
||||
for code, doc in doc_dictionary.items():
|
||||
|
||||
if ProtocolBuilderService.is_enabled():
|
||||
doc['required'] = False
|
||||
if ProtocolBuilderService.is_enabled() and doc['id']:
|
||||
pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None)
|
||||
doc['required'] = False
|
||||
if pb_data:
|
||||
doc['required'] = True
|
||||
|
||||
|
|
@ -282,7 +286,7 @@ class StudyService(object):
|
|||
# Make a display name out of categories
|
||||
name_list = []
|
||||
for cat_key in ['category1', 'category2', 'category3']:
|
||||
if doc[cat_key] not in ['', 'NULL']:
|
||||
if doc[cat_key] not in ['', 'NULL', None]:
|
||||
name_list.append(doc[cat_key])
|
||||
doc['display_name'] = ' / '.join(name_list)
|
||||
|
||||
|
|
@ -319,12 +323,22 @@ class StudyService(object):
|
|||
documents[code] = doc
|
||||
return Box(documents)
|
||||
|
||||
@staticmethod
|
||||
def get_investigator_dictionary():
|
||||
"""Returns a dictionary of document details keyed on the doc_code."""
|
||||
file_data = FileService.get_reference_file_data(StudyService.INVESTIGATOR_LIST)
|
||||
lookup_model = LookupService.get_lookup_model_for_file_data(file_data, 'code', 'label')
|
||||
doc_dict = {}
|
||||
for lookup_data in lookup_model.dependencies:
|
||||
doc_dict[lookup_data.value] = lookup_data.data
|
||||
return doc_dict
|
||||
|
||||
@staticmethod
|
||||
def get_investigators(study_id, all=False):
|
||||
"""Convert array of investigators from protocol builder into a dictionary keyed on the type. """
|
||||
|
||||
# Loop through all known investigator types as set in the reference file
|
||||
inv_dictionary = FileService.get_reference_data(FileService.INVESTIGATOR_LIST, 'code')
|
||||
inv_dictionary = StudyService.get_investigator_dictionary()
|
||||
|
||||
# Get PB required docs
|
||||
pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id)
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ from crc.models.study import StudyModel
|
|||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.user import UserModel, UserModelSchema
|
||||
from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecModel
|
||||
from crc.services.document_service import DocumentService
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.lookup_service import LookupService
|
||||
from crc.services.study_service import StudyService
|
||||
|
|
@ -97,12 +98,15 @@ class WorkflowService(object):
|
|||
def do_waiting():
|
||||
records = db.session.query(WorkflowModel).filter(WorkflowModel.status==WorkflowStatus.waiting).all()
|
||||
for workflow_model in records:
|
||||
print('processing workflow %d'%workflow_model.id)
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.bpmn_workflow.refresh_waiting_tasks()
|
||||
processor.bpmn_workflow.do_engine_steps()
|
||||
processor.save()
|
||||
|
||||
# fixme: Try catch with a very explicit error about the study, workflow and task that failed.
|
||||
try:
|
||||
app.logger.info('Processing workflow %s' % workflow_model.id)
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.bpmn_workflow.refresh_waiting_tasks()
|
||||
processor.bpmn_workflow.do_engine_steps()
|
||||
processor.save()
|
||||
except:
|
||||
app.logger.error('Failed to process workflow')
|
||||
|
||||
@staticmethod
|
||||
@timeit
|
||||
|
|
@ -424,7 +428,7 @@ class WorkflowService(object):
|
|||
doc_code = WorkflowService.evaluate_property('doc_code', field, task)
|
||||
file_model = FileModel(name="test.png",
|
||||
irb_doc_code = field.id)
|
||||
doc_dict = FileService.get_doc_dictionary()
|
||||
doc_dict = DocumentService.get_dictionary()
|
||||
file = File.from_models(file_model, None, doc_dict)
|
||||
return FileSchema().dump(file)
|
||||
elif field.type == 'files':
|
||||
|
|
|
|||
|
|
@ -7,7 +7,9 @@ from crc.models.file import CONTENT_TYPES
|
|||
from crc.models.ldap import LdapModel
|
||||
from crc.models.user import UserModel
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
|
||||
from crc.services.document_service import DocumentService
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.study_service import StudyService
|
||||
|
||||
|
||||
class ExampleDataLoader:
|
||||
|
|
@ -315,14 +317,14 @@ class ExampleDataLoader:
|
|||
def load_reference_documents(self):
|
||||
file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
||||
file = open(file_path, "rb")
|
||||
FileService.add_reference_file(FileService.DOCUMENT_LIST,
|
||||
FileService.add_reference_file(DocumentService.DOCUMENT_LIST,
|
||||
binary_data=file.read(),
|
||||
content_type=CONTENT_TYPES['xls'])
|
||||
file.close()
|
||||
|
||||
file_path = os.path.join(app.root_path, 'static', 'reference', 'investigators.xlsx')
|
||||
file = open(file_path, "rb")
|
||||
FileService.add_reference_file(FileService.INVESTIGATOR_LIST,
|
||||
FileService.add_reference_file(StudyService.INVESTIGATOR_LIST,
|
||||
binary_data=file.read(),
|
||||
content_type=CONTENT_TYPES['xls'])
|
||||
file.close()
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
# IMPORTANT - Environment must be loaded before app, models, etc....
|
||||
import os
|
||||
|
||||
|
||||
os.environ["TESTING"] = "true"
|
||||
|
||||
import json
|
||||
|
|
@ -23,6 +24,7 @@ from crc.services.file_service import FileService
|
|||
from crc.services.study_service import StudyService
|
||||
from crc.services.user_service import UserService
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
from crc.services.document_service import DocumentService
|
||||
from example_data import ExampleDataLoader
|
||||
|
||||
# UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
|
||||
|
|
@ -138,8 +140,7 @@ class BaseTest(unittest.TestCase):
|
|||
delete everything that matters in the local database - this is used to
|
||||
test ground zero copy of workflow specs.
|
||||
"""
|
||||
session.execute("delete from workflow; delete from file_data; delete from file; delete from workflow_spec;")
|
||||
session.commit()
|
||||
ExampleDataLoader.clean_db()
|
||||
|
||||
def load_example_data(self, use_crc_data=False, use_rrt_data=False):
|
||||
"""use_crc_data will cause this to load the mammoth collection of documents
|
||||
|
|
@ -282,28 +283,6 @@ class BaseTest(unittest.TestCase):
|
|||
session.commit()
|
||||
return study
|
||||
|
||||
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
|
||||
workflow_spec_name="random_fact"):
|
||||
study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
|
||||
workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
|
||||
approvals = []
|
||||
|
||||
for i in range(len(approver_uids)):
|
||||
approvals.append(self.create_approval(
|
||||
study=study,
|
||||
workflow=workflow,
|
||||
approver_uid=approver_uids[i],
|
||||
status=statuses[i],
|
||||
version=1
|
||||
))
|
||||
|
||||
full_study = {
|
||||
'study': study,
|
||||
'workflow': workflow,
|
||||
'approvals': approvals,
|
||||
}
|
||||
|
||||
return full_study
|
||||
|
||||
def create_workflow(self, workflow_name, display_name=None, study=None, category_id=None, as_user="dhf8r"):
|
||||
session.flush()
|
||||
|
|
@ -320,30 +299,11 @@ class BaseTest(unittest.TestCase):
|
|||
def create_reference_document(self):
|
||||
file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
||||
file = open(file_path, "rb")
|
||||
FileService.add_reference_file(FileService.DOCUMENT_LIST,
|
||||
FileService.add_reference_file(DocumentService.DOCUMENT_LIST,
|
||||
binary_data=file.read(),
|
||||
content_type=CONTENT_TYPES['xls'])
|
||||
content_type=CONTENT_TYPES['xlsx'])
|
||||
file.close()
|
||||
|
||||
def create_approval(
|
||||
self,
|
||||
study=None,
|
||||
workflow=None,
|
||||
approver_uid=None,
|
||||
status=None,
|
||||
version=None,
|
||||
):
|
||||
study = study or self.create_study()
|
||||
workflow = workflow or self.create_workflow()
|
||||
approver_uid = approver_uid or self.test_uid
|
||||
status = status or ApprovalStatus.PENDING.value
|
||||
version = version or 1
|
||||
approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status,
|
||||
version=version)
|
||||
session.add(approval)
|
||||
session.commit()
|
||||
return approval
|
||||
|
||||
def get_workflow_common(self, url, user):
|
||||
rv = self.app.get(url,
|
||||
headers=self.logged_in_headers(user),
|
||||
|
|
|
|||
|
|
@ -16,6 +16,12 @@
|
|||
OGC will upload the Non-Funded Executed Agreement after it has been negotiated by OSP contract negotiator.</bpmn:documentation>
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
<camunda:formField id="Date" label="Version Date" type="date">
|
||||
<camunda:properties>
|
||||
<camunda:property id="group" value="PCRApproval" />
|
||||
<camunda:property id="file_data" value="Some_File" />
|
||||
</camunda:properties>
|
||||
</camunda:formField>
|
||||
<camunda:formField id="file_type" type="enum" defaultValue="AD_CoCApp">
|
||||
<camunda:value id="AD_CoCApp" name="Ancillary Documents / Case Report Form" />
|
||||
<camunda:value id="AD_CoCAppr" name="Ancillary Documents / CoC Approval" />
|
||||
|
|
@ -32,12 +38,6 @@ OGC will upload the Non-Funded Executed Agreement after it has been negotiated b
|
|||
<camunda:property id="file_data" value="Some_File" />
|
||||
</camunda:properties>
|
||||
</camunda:formField>
|
||||
<camunda:formField id="Date" label="Version Date" type="date">
|
||||
<camunda:properties>
|
||||
<camunda:property id="group" value="PCRApproval" />
|
||||
<camunda:property id="file_data" value="Some_File" />
|
||||
</camunda:properties>
|
||||
</camunda:formField>
|
||||
</camunda:formData>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_0ea9hvd</bpmn:incoming>
|
||||
|
|
@ -67,4 +67,4 @@ OGC will upload the Non-Funded Executed Agreement after it has been negotiated b
|
|||
</bpmndi:BPMNShape>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
</bpmn:definitions>
|
||||
|
|
@ -1,14 +1,16 @@
|
|||
import io
|
||||
import json
|
||||
import os
|
||||
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
from crc import session, db
|
||||
from crc import session, db, app
|
||||
from crc.models.file import FileModel, FileType, FileSchema, FileModelSchema
|
||||
from crc.models.workflow import WorkflowSpecModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.models.data_store import DataStoreModel
|
||||
from crc.services.document_service import DocumentService
|
||||
from example_data import ExampleDataLoader
|
||||
|
||||
|
||||
|
|
@ -110,20 +112,23 @@ class TestFilesApi(BaseTest):
|
|||
self.assertEqual(0, len(json.loads(rv.get_data(as_text=True))))
|
||||
|
||||
def test_set_reference_file(self):
|
||||
file_name = "irb_document_types.xls"
|
||||
data = {'file': (io.BytesIO(b"abcdef"), "does_not_matter.xls")}
|
||||
file_name = "irb_documents.xlsx"
|
||||
filepath = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
||||
with open(filepath, 'rb') as myfile:
|
||||
file_data = myfile.read()
|
||||
data = {'file': (io.BytesIO(file_data), file_name)}
|
||||
rv = self.app.put('/v1.0/reference_file/%s' % file_name, data=data, follow_redirects=True,
|
||||
content_type='multipart/form-data', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
self.assertIsNotNone(rv.get_data())
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
file = FileModelSchema().load(json_data, session=session)
|
||||
self.assertEqual(FileType.xls, file.type)
|
||||
self.assertEqual(FileType.xlsx, file.type)
|
||||
self.assertTrue(file.is_reference)
|
||||
self.assertEqual("application/vnd.ms-excel", file.content_type)
|
||||
self.assertEqual("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", file.content_type)
|
||||
|
||||
def test_set_reference_file_bad_extension(self):
|
||||
file_name = FileService.DOCUMENT_LIST
|
||||
file_name = DocumentService.DOCUMENT_LIST
|
||||
data = {'file': (io.BytesIO(b"abcdef"), "does_not_matter.ppt")}
|
||||
rv = self.app.put('/v1.0/reference_file/%s' % file_name, data=data, follow_redirects=True,
|
||||
content_type='multipart/form-data', headers=self.logged_in_headers())
|
||||
|
|
@ -131,22 +136,28 @@ class TestFilesApi(BaseTest):
|
|||
|
||||
def test_get_reference_file(self):
|
||||
file_name = "irb_document_types.xls"
|
||||
data = {'file': (io.BytesIO(b"abcdef"), "some crazy thing do not care.xls")}
|
||||
filepath = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
||||
with open(filepath, 'rb') as myfile:
|
||||
file_data = myfile.read()
|
||||
data = {'file': (io.BytesIO(file_data), file_name)}
|
||||
rv = self.app.put('/v1.0/reference_file/%s' % file_name, data=data, follow_redirects=True,
|
||||
content_type='multipart/form-data', headers=self.logged_in_headers())
|
||||
rv = self.app.get('/v1.0/reference_file/%s' % file_name, headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
data_out = rv.get_data()
|
||||
self.assertEqual(b"abcdef", data_out)
|
||||
self.assertEqual(file_data, data_out)
|
||||
|
||||
def test_list_reference_files(self):
|
||||
ExampleDataLoader.clean_db()
|
||||
|
||||
file_name = FileService.DOCUMENT_LIST
|
||||
data = {'file': (io.BytesIO(b"abcdef"), file_name)}
|
||||
file_name = DocumentService.DOCUMENT_LIST
|
||||
filepath = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
||||
with open(filepath, 'rb') as myfile:
|
||||
file_data = myfile.read()
|
||||
data = {'file': (io.BytesIO(file_data), file_name)}
|
||||
rv = self.app.put('/v1.0/reference_file/%s' % file_name, data=data, follow_redirects=True,
|
||||
content_type='multipart/form-data', headers=self.logged_in_headers())
|
||||
|
||||
self.assert_success(rv)
|
||||
rv = self.app.get('/v1.0/reference_file',
|
||||
follow_redirects=True,
|
||||
content_type="application/json", headers=self.logged_in_headers())
|
||||
|
|
@ -159,7 +170,8 @@ class TestFilesApi(BaseTest):
|
|||
|
||||
def test_update_file_info(self):
|
||||
self.load_example_data()
|
||||
file: FileModel = session.query(FileModel).first()
|
||||
self.create_reference_document()
|
||||
file: FileModel = session.query(FileModel).filter(FileModel.is_reference==False).first()
|
||||
file.name = "silly_new_name.bpmn"
|
||||
|
||||
rv = self.app.put('/v1.0/file/%i' % file.id,
|
||||
|
|
|
|||
|
|
@ -1,4 +1,3 @@
|
|||
import json
|
||||
|
||||
from SpiffWorkflow.bpmn.PythonScriptEngine import Box
|
||||
|
||||
|
|
@ -15,6 +14,7 @@ from crc.services.file_service import FileService
|
|||
from crc.services.study_service import StudyService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.scripts.file_data_set import FileDataSet
|
||||
from crc.services.document_service import DocumentService
|
||||
|
||||
|
||||
class TestStudyDetailsDocumentsScript(BaseTest):
|
||||
|
|
@ -43,8 +43,8 @@ class TestStudyDetailsDocumentsScript(BaseTest):
|
|||
|
||||
# Remove the reference file.
|
||||
file_model = db.session.query(FileModel). \
|
||||
filter(FileModel.is_reference == True). \
|
||||
filter(FileModel.name == FileService.DOCUMENT_LIST).first()
|
||||
filter(FileModel.is_reference is True). \
|
||||
filter(FileModel.name == DocumentService.DOCUMENT_LIST).first()
|
||||
if file_model:
|
||||
db.session.query(FileDataModel).filter(FileDataModel.file_model_id == file_model.id).delete()
|
||||
db.session.query(FileModel).filter(FileModel.id == file_model.id).delete()
|
||||
|
|
@ -71,7 +71,7 @@ class TestStudyDetailsDocumentsScript(BaseTest):
|
|||
|
||||
def test_load_lookup_data(self):
|
||||
self.create_reference_document()
|
||||
dict = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
|
||||
dict = DocumentService.get_dictionary()
|
||||
self.assertIsNotNone(dict)
|
||||
|
||||
def get_required_docs(self):
|
||||
|
|
|
|||
|
|
@ -122,11 +122,11 @@ class TestStudyService(BaseTest):
|
|||
self.assertEqual("Cancer Center's PRC Approval Form", documents["UVACompl_PRCAppr"]['description'])
|
||||
self.assertEqual("UVA Compliance", documents["UVACompl_PRCAppr"]['category1'])
|
||||
self.assertEqual("PRC Approval", documents["UVACompl_PRCAppr"]['category2'])
|
||||
self.assertEqual("", documents["UVACompl_PRCAppr"]['category3'])
|
||||
self.assertEqual(None, documents["UVACompl_PRCAppr"]['category3'])
|
||||
self.assertEqual("CRC", documents["UVACompl_PRCAppr"]['Who Uploads?'])
|
||||
self.assertEqual(0, documents["UVACompl_PRCAppr"]['count'])
|
||||
self.assertEqual(True, documents["UVACompl_PRCAppr"]['required'])
|
||||
self.assertEqual('6', documents["UVACompl_PRCAppr"]['id'])
|
||||
self.assertEqual(6, documents["UVACompl_PRCAppr"]['id'])
|
||||
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
||||
def test_get_documents_has_file_details(self, mock_docs):
|
||||
|
|
|
|||
|
|
@ -3,9 +3,6 @@ from tests.base_test import BaseTest
|
|||
from crc.services.file_service import FileService
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
class TestDocumentDirectories(BaseTest):
|
||||
|
||||
def test_directory_list(self):
|
||||
|
|
|
|||
Loading…
Reference in New Issue