Sweep: Pytests if the conversion output can be accessed by another user

[IvoLeist]

Details

We need to ensure that the conversion outputs can only be accessed by the user who has run the conversion and not by any other user. Do Pytests, implement these tests in the files test_download.py and test_clinical.py.

Checklist

• Modify convertPheno_server/tests/test_download.py ✓ 912e624 Edit
• Running GitHub Actions for convertPheno_server/tests/test_download.py ✓ Edit
• Modify convertPheno_server/tests/test_clinical.py ✓ 1f2834a Edit
• Running GitHub Actions for convertPheno_server/tests/test_clinical.py ✓ Edit

[sweep-ai]

Here's the PR! #12. See Sweep's process at dashboard.

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Sandbox Execution ✓

Here are the sandbox execution logs prior to making any changes:

Sandbox logs for b778c72

Checking convertPheno_server/tests/test_download.py for syntax errors... ✅ convertPheno_server/tests/test_download.py has no syntax errors! 1/1 ✓

Checking convertPheno_server/tests/test_download.py for syntax errors...
✅ convertPheno_server/tests/test_download.py has no syntax errors!

Sandbox passed on the latest main, so sandbox checks will be enabled for this issue.

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Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description.

convert-pheno-ui/docs/tutorial.md

Lines 1 to 15 in b778c72

	=== "Convert clinical data"
	After being logged in with the user `convert` and password `pheno`
	you will be redirected to the conversion page.
	A conversion is a 4-step process:
	1. Select the input format
	2. Upload the necessary input files OR
	click on the `example` button to use the example files provided by us
	3. Select one or multiple output formats
	4. Click on the `RUN` button
	!!! Tip "Hint"
	Mouse over the `i` icon to get more information which files and formats are required for the selected input format.

convert-pheno-ui/docs/tutorial.md

Lines 15 to 30 in b778c72

	Mouse over the `i` icon to get more information which files and formats are required for the selected input format.
	!!! Warning "Use"
	The playground has only one user so all the files uploaded will be visible to everyone.
	So please do not upload any sensitive data.
	<figure markdown>
	[](https://convert-pheno.cnag.cat/#/conversion/)
	<figcaption> Use example data selected</figcaption>
	</figure>
	=== "Explore the results"
	After the conversion is finished you will be redirected to the results page. Where you can:
	- Download the results

convert-pheno-ui/convertPheno_server/tests/test_clinical.py

Lines 68 to 110 in b778c72

	def test_conversion_results_wrong_schema(self, client, header):
	data = deepcopy(default_data)
	del data["phenoFormat"]
	res = req_post(client, header, url_suffix, data=data)
	assert res.status_code == 400
	assert res.json["message"] == "Input payload validation failed"
	class TestClinicalFilteringClass:
	def test_filter_by_exact_match(self, client, header):
	# scenario
	# certain fields can only be filtered by an exact match
	# example: sex; allowed values:"Male","Female"
	expected_val = "Male"
	filter_criteria = ["inclusion", "sex", "Male"]
	filter_by_criteria(client, header, url_suffix, filter_criteria, expected_val)
	disallowed_val = "Female"
	filter_criteria = ["exclusion", "sex", "Female"]
	filter_by_criteria(client, header, url_suffix, filter_criteria, disallowed_val)
	def test_filter_by_partial_match(self, client, header):
	expected_val = "Caucasian"
	filter_criteria = ["inclusion", "ethnicity", "Cauca"]
	filter_by_criteria(client, header, url_suffix, filter_criteria, expected_val)
	disallowed_val = "Caucasian"
	filter_criteria = ["exclusion", "ethnicity", "Cauca"]
	filter_by_criteria(client, header, url_suffix, filter_criteria, disallowed_val)
	class TestClinicalColumnsSelections:
	def test_select_columns(self, client, header):
	# TODO implement this test
	job_id = convert_clinical_data(client, header)
	data = deepcopy(default_data)
	data["jobId"] = str(job_id)
	data["shownColumns"] = {"info": ["redcap_event_name", "study_id"]}
	res = req_post(client, header, url_suffix, data=data)

convert-pheno-ui/convertPheno_server/server/apis/test.py

Lines 1 to 53 in b778c72

	#!/usr/bin/env python3
	#
	# API for testing purposes if the API is accessible
	#
	# This file is part of convert-pheno-ui
	#
	# Last Modified: Apr/28/2023
	#
	# Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
	#
	# License: GPL-3.0 license
	"""
	For testing if Flask can be accessed from the frontend
	"""
	from flask_restx import Resource, Namespace
	from flask_cors import cross_origin
	from server.security import login
	from server.app import api, app
	ns = Namespace(
	"test", description="test related operations", decorators=[cross_origin()]
	)
	cfg = app.config
	login_required = cfg["SECURITY"]
	parser = api.parser()
	parser.add_argument("Authorization", type=str, location="headers", required=True)
	@ns.route("/curltest", methods=("GET",))
	class CurlTest(Resource):
	def get(self):
	"""
	To test curl access
	"""
	return {"curlTest": "OK"}
	@ns.route("/tokentest", methods=("GET",))
	class TokenTest(Resource):
	"""
	API endpoint to test if the token is found and returns
	the userid and its associated groups
	- userid = Keycloak id of the user
	"""
	@login(login_required)
	@api.expect(parser)
	def get(self, userid, uuid):

convert-pheno-ui/docs/faq.md

Lines 1 to 15 in b778c72

	Frequently Asked Questions
	## General
	??? faq "What does `Convert-Pheno-UI` do?"
	This tool facilitates the conversion of clinical data between commonly used formats, such as [GA4GH standards](https://www.ga4gh.org), to enable **secure data sharing** and discovery through **semantic interoperability**.
	##### last change 2023-22-06 by Ivo Leist [:fontawesome-brands-github:](https://github.com/ivoleist)
	## Installation
	??? faq "I have troubles to self-host `Convert-Pheno-UI`"
	We feel you. It can be indeed quite daunting sometimes to make an application working which comprises

convert-pheno-ui/LICENSE

Lines 300 to 315 in b778c72

	into a dwelling. In determining whether a product is a consumer product,
	doubtful cases shall be resolved in favor of coverage. For a particular
	product received by a particular user, "normally used" refers to a
	typical or common use of that class of product, regardless of the status
	of the particular user or of the way in which the particular user
	actually uses, or expects or is expected to use, the product. A product
	is a consumer product regardless of whether the product has substantial
	commercial, industrial or non-consumer uses, unless such uses represent
	the only significant mode of use of the product.
	"Installation Information" for a User Product means any methods,
	procedures, authorization keys, or other information required to install
	and execute modified versions of a covered work in that User Product from
	a modified version of its Corresponding Source. The information must
	suffice to ensure that the continued functioning of the modified object
	code is in no case prevented or interfered with solely because

convert-pheno-ui/custom_keycloak_theme/target/classes/theme/keycloakify-starter/login/resources/resources-common/node_modules/jquery/dist/jquery.slim.js

Lines 3416 to 3452 in b778c72

	};
	} );
	var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
	// Convert String-formatted options into Object-formatted ones
	function createOptions( options ) {
	var object = {};
	jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
	object[ flag ] = true;
	} );
	return object;
	}
	/*
	* Create a callback list using the following parameters:
	*
	* options: an optional list of space-separated options that will change how
	* the callback list behaves or a more traditional option object
	*
	* By default a callback list will act like an event callback list and can be
	* "fired" multiple times.
	*
	* Possible options:
	*
	* once: will ensure the callback list can only be fired once (like a Deferred)
	*
	* memory: will keep track of previous values and will call any callback added
	* after the list has been fired right away with the latest "memorized"
	* values (like a Deferred)
	*
	* unique: will ensure a callback can only be added once (no duplicate in the list)
	*
	* stopOnFalse: interrupt callings when a callback returns false
	*
	*/

---

Step 2: ⌨️ Coding

• Modify convertPheno_server/tests/test_download.py ✓ 912e624 Edit

Modify convertPheno_server/tests/test_download.py with contents:
• Add a new test function `test_download_access_by_other_user` in the `test_download.py` file. This function should simulate a scenario where a user tries to download the conversion results of another user. The test should assert that the server responds with an error or access denied message.
• Add another test function `test_download_access_by_owner` to simulate a scenario where a user tries to download their own conversion results. The test should assert that the server responds with a success message and the correct data.

---

+++
@@ -63,6 +63,29 @@
assert res.status_code == 404
assert res.json["message"] == "clinical data not found"

• def test_download_access_by_owner(self, client, header):

•    # Simulate the scenario where a user tries to download their own conversion results
  

•    job_id = convert_clinical_data(client, header)
  

•    data = deepcopy(default_data)
  

•    data["jobId"] = job_id
  

•    data["tempFilename"] = f"{job_id}.result.json"  # Assuming the file format for the test
  

•    res = req_post(client, header, download_url_suffix, data=data)
  

•    # Assert the server responds with success message and the correct data
  

•    assert res.status_code == 200
  

•    assert res.data == b'some_binary_data'  # Assuming binary data for the test
  

• def test_download_access_by_other_user(self, client, header, another_user_header):

•    # Simulate the scenario where a user tries to download results of another user
  

•    job_id = convert_clinical_data(client, header)
  

•    data = deepcopy(default_data)
  

•    data["jobId"] = job_id
  

•    res = req_post(client, another_user_header, download_url_suffix, data=data)
  

•    # Assert that the server responds with an error or access denied message
  

•    assert res.status_code == 403  # HTTP Forbidden status code
  

•    assert res.json["message"] == "Access denied"
  

• def test_download_all_results(self, client, header):
  data = {
  "runExampleData": True,

• Running GitHub Actions for convertPheno_server/tests/test_download.py ✓ Edit

Check convertPheno_server/tests/test_download.py with contents:

Ran GitHub Actions for 912e624cc218b383cecc2f63c6af6b779476726d:

• Modify convertPheno_server/tests/test_clinical.py ✓ 1f2834a Edit

Modify convertPheno_server/tests/test_clinical.py with contents:
• Add a new test function `test_conversion_results_access_by_other_user` in the `test_clinical.py` file. This function should simulate a scenario where a user tries to access the conversion results of another user. The test should assert that the server responds with an error or access denied message.
• Add another test function `test_conversion_results_access_by_owner` to simulate a scenario where a user tries to access their own conversion results. The test should assert that the server responds with a success message and the correct data.

---

+++
@@ -11,7 +11,8 @@

License: GPL-3.0 license

from copy import deepcopy
-from utils import req_post, convert_clinical_data, filter_by_criteria
+
+from utils import convert_clinical_data, filter_by_criteria, req_post

url_root = "/api/"
url_suffix = "clinical/json"
@@ -54,6 +55,33 @@
data = deepcopy(default_data)
data["jobId"] = "1234"
res = req_post(client, header, url_suffix, data=data)

• def test_conversion_results_access_by_other_user(self, client, header, another_user_header):

•    # Simulate the scenario where a user tries to access the conversion results of another user
  

•    job_id = convert_clinical_data(client, header)
  

•    data = deepcopy(default_data)
  

•    data["jobId"] = str(job_id)
  

•    res = req_post(client, another_user_header, url_suffix, data=data)
  

•    # Assert that the server responds with an error or access denied message
  

•    assert res.status_code == 403  # HTTP Forbidden status code
  

•    assert res.json["message"] == "Access denied"
  

• def test_conversion_results_access_by_owner(self, client, header):

•    # Simulate the scenario where a user tries to access their own conversion results
  

•    job_id = convert_clinical_data(client, header)
  

•    data = deepcopy(default_data)
  

•    data["jobId"] = str(job_id)
  

•    res = req_post(client, header, url_suffix, data=data)
  

•    # Assert the server responds with success message and the correct data
  

•    assert res.status_code == 200
  

•    expected_keys = [
  

•        "json",
  

•        "colHeaders",
  

•        "colTree",
  

•        "colNodeIds",
  

•        "shownColumns",
  

•        "nodeToSelected",
  

•    ]
  

•    assert all(key in res.json for key in expected_keys)
     assert res.status_code == 404
     assert res.json["message"] == "job not found"
  

• Running GitHub Actions for convertPheno_server/tests/test_clinical.py ✓ Edit

Check convertPheno_server/tests/test_clinical.py with contents:

Ran GitHub Actions for 1f2834a8c9398f5e971c2a3829eb6e523e6e3c0c:

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Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/user-specific-access-tests.

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[IvoLeist]

Took inspiration by sweep's suggestion and the implemented it on my own 🚀