From ecff7d20d3ff085a1da4fc948bdf39de8eb7bf83 Mon Sep 17 00:00:00 2001 From: Dan Date: Wed, 21 Apr 2021 14:00:19 -0400 Subject: [PATCH] Adding a test for the new endpoint and cleaning up the API documenation --- crc/api.yml | 45 ++- crc/api/file.py | 31 +- crc/models/api_models.py | 1 + postgres/package-lock.json | 480 ++++++++++++++++++++++++++++- tests/test_document_directories.py | 41 +++ 5 files changed, 556 insertions(+), 42 deletions(-) create mode 100644 tests/test_document_directories.py diff --git a/crc/api.yml b/crc/api.yml index 289ad153..24e4efdf 100644 --- a/crc/api.yml +++ b/crc/api.yml @@ -94,11 +94,9 @@ paths: content: application/json: schema: - type: object - properties: - Admin: - schema: - $ref: "#/components/schemas/DocumentCategories" + type: array + items: + $ref: "#/components/schemas/DocumentDirectory" # /v1.0/study /study: @@ -1462,34 +1460,29 @@ components: type: string x-nullable: true example: "27b-6-1212" - DocumentCategories: + DocumentDirectory: properties: - category1: + level: type: string x-nullable: true example: "Ancillary Document" - category2: - type: string - x-nullable: true - example: "Lab Manual" - category3: - type: string - x-nullable: true - example: "" - Who Uploads?: - type: string - x-nullable: true - example: "CRC" description: type: string x-nullable: true - example: "some description" - - - - - - + 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: diff --git a/crc/api/file.py b/crc/api/file.py index 1fd8349a..33977533 100644 --- a/crc/api/file.py +++ b/crc/api/file.py @@ -11,7 +11,8 @@ from crc.models.api_models import DocumentDirectory, DocumentDirectorySchema from crc.models.workflow import WorkflowSpecModel from crc.services.file_service import FileService -def ensure_exists(output,categories,expanded): + +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) @@ -21,28 +22,28 @@ def ensure_exists(output,categories,expanded): function terminates upon getting an entry that is a file object ( or really anything but string) """ - currentitem = categories[0] + current_item = categories[0] found = False - if isinstance(currentitem,str): + if isinstance(current_item, str): for item in output: - if item.level == currentitem: + if item.level == current_item: found = True item.filecount = item.filecount + 1 item.expanded = expanded | item.expanded - ensure_exists(item.children,categories[1:],expanded) + ensure_exists(item.children, categories[1:], expanded) if not found: - newlevel = DocumentDirectory(level=currentitem) - newlevel.filecount = 1 - newlevel.expanded = expanded - output.append(newlevel) - ensure_exists(newlevel.children,categories[1:],expanded) + 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: - newlevel = DocumentDirectory(file=currentitem) - newlevel.expanded = expanded - output.append(newlevel) + new_level = DocumentDirectory(file=current_item) + new_level.expanded = expanded + output.append(new_level) -def get_document_directory(study_id,workflow_id=None): +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 @@ -59,7 +60,7 @@ def get_document_directory(study_id,workflow_id=None): 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) + ensure_exists(output, categories, expanded=expand) return DocumentDirectorySchema(many=True).dump(output) diff --git a/crc/models/api_models.py b/crc/models/api_models.py index 74c0bc2b..2bb4abc6 100644 --- a/crc/models/api_models.py +++ b/crc/models/api_models.py @@ -174,6 +174,7 @@ class DocumentDirectorySchema(ma.Schema): expanded = marshmallow.fields.Boolean() children = marshmallow.fields.Nested("self",many=True) + class DocumentDirectory(object): def __init__(self, level=None, file=None, children=None): diff --git a/postgres/package-lock.json b/postgres/package-lock.json index 48e341a0..88665a72 100644 --- a/postgres/package-lock.json +++ b/postgres/package-lock.json @@ -1,3 +1,481 @@ { - "lockfileVersion": 1 + "requires": true, + "lockfileVersion": 1, + "dependencies": { + "@types/node": { + "version": "14.14.41", + "resolved": "https://registry.npmjs.org/@types/node/-/node-14.14.41.tgz", + "integrity": "sha512-dueRKfaJL4RTtSa7bWeTK1M+VH+Gns73oCgzvYfHZywRCoPSd8EkXBL0mZ9unPTveBn+D9phZBaxuzpwjWkW0g==", + "dev": 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b/tests/test_document_directories.py new file mode 100644 index 00000000..151729d9 --- /dev/null +++ b/tests/test_document_directories.py @@ -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'])