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Merge pull request #292 from sartography/277-Document-pane

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277 document pane
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Dan Funk 2021-04-21 17:28:41 -04:00 committed by GitHub
commit 63dcb4599e
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9 changed files with 695 additions and 11 deletions
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60
crc/api.yml
View File

@ -67,6 +67,37 @@ paths:
type: array
items:
$ref: "#/components/schemas/User"
# /v1.0/document_directory/{study_id}
/document_directory/{study_id}:
parameters :
- name : study_id
required : true
in : path
description : The unique id of a study.
schema :
type : integer
- name : workflow_id
in : query
required : false
schema :
type : integer
get:
operationId: crc.api.file.get_document_directory
security:
- auth_admin: ['secret']
summary: Returns a directory of all files for study in a nested structure
tags:
- Document Categories
responses:
'200':
description: All IRB Categories defined in the file document.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/DocumentDirectory"
# /v1.0/study
/study:
get:
@ -565,6 +596,12 @@ paths:
description: The unique key of a workflow task form field. Make sure this matches a document in the irb_documents.xslx reference sheet.
schema:
type: string
- name: study_id
in: query
required: false
description: The study that the files are related to
schema:
type: integer
get:
operationId: crc.api.file.get_files
summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
@ -1429,6 +1466,29 @@ components:
type: string
x-nullable: true
example: "27b-6-1212"
DocumentDirectory:
properties:
level:
type: string
x-nullable: true
example: "Ancillary Document"
description:
type: string
x-nullable: true
example: "Documents that are ancillary to the study"
file:
$ref: "#/components/schemas/File"
x-nullable: true
expanded:
type: boolean
example: False
filecount:
type: integer
example: 1
children:
type: array
items:
$ref: "#/components/schemas/File"
DataStore:
properties:
id:

60
crc/api/file.py
View File

@ -6,23 +6,79 @@ from flask import send_file
from crc import session
from crc.api.common import ApiError
from crc.models.api_models import DocumentDirectory, DocumentDirectorySchema
from crc.models.file import FileSchema, FileModel, File, FileModelSchema, FileDataModel, FileType
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
def ensure_exists(output, categories, expanded):
"""
This is a recursive function, it expects a list of
levels with a file object at the end (kinda like duck,duck,duck,goose)
for each level, it makes sure that level is already in the structure and if it is not
it will add it
function terminates upon getting an entry that is a file object ( or really anything but string)
"""
current_item = categories[0]
found = False
if isinstance(current_item, str):
for item in output:
if item.level == current_item:
found = True
item.filecount = item.filecount + 1
item.expanded = expanded | item.expanded
ensure_exists(item.children, categories[1:], expanded)
if not found:
new_level = DocumentDirectory(level=current_item)
new_level.filecount = 1
new_level.expanded = expanded
output.append(new_level)
ensure_exists(new_level.children, categories[1:], expanded)
else:
new_level = DocumentDirectory(file=current_item)
new_level.expanded = expanded
output.append(new_level)
def get_document_directory(study_id, workflow_id=None):
"""
return a nested list of files arranged according to the category hirearchy
defined in the doc dictionary
"""
output = []
doc_dict = FileService.get_doc_dictionary()
file_models = FileService.get_files_for_study(study_id=study_id)
files = (to_file_api(model) for model in file_models)
for file in files:
doc_code = doc_dict[file.irb_doc_code]
if workflow_id:
expand = file.workflow_id == int(workflow_id)
else:
expand = False
print(expand)
categories = [x for x in [doc_code['category1'],doc_code['category2'],doc_code['category3'],file] if x != '']
ensure_exists(output, categories, expanded=expand)
return DocumentDirectorySchema(many=True).dump(output)
def to_file_api(file_model):
"""Converts a FileModel object to something we can return via the api"""
return File.from_models(file_model, FileService.get_file_data(file_model.id),
FileService.get_doc_dictionary())
def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None):
if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key]):
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 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)
else:
file_models = FileService.get_files(workflow_spec_id=workflow_spec_id,
workflow_id=workflow_id,
irb_doc_code=form_field_key)

23
crc/models/api_models.py
View File

@ -7,7 +7,7 @@ from marshmallow_enum import EnumField
from crc import ma
from crc.models.workflow import WorkflowStatus
from crc.models.file import FileSchema
class MultiInstanceType(enum.Enum):
none = "none"
@ -167,6 +167,27 @@ class NavigationItemSchema(ma.Schema):
item.spec_type = spec_type
return item
class DocumentDirectorySchema(ma.Schema):
level = marshmallow.fields.String()
file = marshmallow.fields.Nested(FileSchema)
filecount = marshmallow.fields.Integer()
expanded = marshmallow.fields.Boolean()
children = marshmallow.fields.Nested("self",many=True)
class DocumentDirectory(object):
def __init__(self, level=None, file=None, children=None):
self.level = level
self.file = file
self.expanded = False
self.filecount = 0
if children is None:
self.children = list()
else:
self.children=children
class WorkflowApi(object):
def __init__(self, id, status, next_task, navigation,
spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks,

2
crc/models/file.py
View File

@ -108,7 +108,7 @@ class File(object):
doc_dictionary[model.irb_doc_code]['category2'],
doc_dictionary[model.irb_doc_code]['category3']]))
instance.description = doc_dictionary[model.irb_doc_code]['description']
instance.download_name = ".".join([instance.category, model.type.value])
instance.download_name = "/".join([instance.category, model.name])
else:
instance.category = ""
instance.description = ""

32
crc/services/file_service.py
View File

@ -17,6 +17,21 @@ from crc.api.common import ApiError
from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecDependencyFile
from crc.services.cache_service import cache
import re
def camel_to_snake(camel):
"""
make a camelcase from a snakecase
with a few things thrown in - we had a case where
we were parsing a spreadsheet and using the headings as keys in an object
one of the headings was "Who Uploads?"
"""
camel = camel.strip()
camel = re.sub(' ', '', camel)
camel = re.sub('?', '', camel)
return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
class FileService(object):
"""Provides consistent management and rules for storing, retrieving and processing files."""
@ -25,10 +40,27 @@ class FileService(object):
__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

4
crc/services/workflow_processor.py
View File

@ -98,10 +98,6 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
@staticmethod
def camel_to_snake(camel):
camel = camel.strip()
return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
class MyCustomParser(BpmnDmnParser):

480
postgres/package-lock.json generated
View File

@ -1,3 +1,481 @@
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2
tests/study/test_study_api.py
View File

@ -97,7 +97,7 @@ class TestStudyApi(BaseTest):
self.assertEqual(1, len(study.files))
self.assertEqual("UVA Compliance/PRC Approval", study.files[0]["category"])
self.assertEqual("Cancer Center's PRC Approval Form", study.files[0]["description"])
self.assertEqual("UVA Compliance/PRC Approval.png", study.files[0]["download_name"])
self.assertEqual("UVA Compliance/PRC Approval/anything.png", study.files[0]["download_name"])
# TODO: WRITE A TEST FOR STUDY FILES

41
tests/test_document_directories.py Normal file
View File

@ -0,0 +1,41 @@
import json
from tests.base_test import BaseTest
from crc.services.file_service import FileService
class TestDocumentDirectories(BaseTest):
def test_directory_list(self):
self.load_example_data()
irb_code_1 = 'UVACompl_PRCAppr'
irb_code_2 = 'Study_App_Doc'
workflow = self.create_workflow('empty_workflow')
first_task = self.get_workflow_api(workflow).next_task
study_id = workflow.study_id
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
name="something.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code_1)
# Add second file
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code=irb_code_2)
# Get back the list of documents and their directories.
rv = self.app.get('/v1.0/document_directory/%i' % study_id, headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
print(json_data)
self.assertEquals(2, len(json_data))
self.assertEquals('UVA Compliance', json_data[0]['level'])
self.assertEquals('PRC Approval', json_data[0]['children'][0]['level'])
self.assertEquals('something.png', json_data[0]['children'][0]['children'][0]['file']['name'])
self.assertEquals('Study', json_data[1]['level'])
self.assertEquals('Application', json_data[1]['children'][0]['level'])
self.assertEquals('Document', json_data[1]['children'][0]['children'][0]['level'])
self.assertEquals('anything.png', json_data[1]['children'][0]['children'][0]['children'][0]['file']['name'])