diff options
| -rw-r--r-- | .github/ISSUE_TEMPLATE/bug_report.md | 3 | ||||
| -rw-r--r-- | .github/workflows/main.yml | 31 | ||||
| -rw-r--r-- | README.md | 11 | ||||
| -rw-r--r-- | doc/docker-container.org | 86 | ||||
| -rw-r--r-- | test/requests/main_web_functionality.py | 2 | ||||
| -rw-r--r-- | wqflask/tests/base/test_data_set.py | 10 | ||||
| -rw-r--r-- | wqflask/tests/base/test_trait.py | 101 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_authentication_tools.py | 193 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_hmac.py | 39 | ||||
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 41 | ||||
| -rw-r--r-- | wqflask/utility/hmac.py | 9 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 120 |
12 files changed, 581 insertions, 65 deletions
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 789d6a57..7d7e34a5 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -26,7 +26,8 @@ If applicable, add screenshots to help explain your problem. **Environment setup (please complete the following information):** - OS: [e.g. Linux] -- Racket Version [e.g. v7.6] +- Guix Version (optional) +- [Anything else you think is relevant] **Additional context** diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..4c8db1c4 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,31 @@ +name: tests + +# Run actions when pushing to the testing branch or when you create a +# PR against it +on: + push: + branches: [ testing ] + pull_request: + branches: [ testing ] + +jobs: + unittest: + runs-on: ubuntu-latest + container: bonfacekilz/python2-genenetwork2:latest + + steps: + # Use v1 of checkout since v2 fails + - name: Checkout Project + uses: actions/checkout@v1 + + # Redis is required by some of the tests + - name: Start Redis + run: | + redis-server --daemonize yes + + - name: Run the unit tests + run: | + mkdir -p /genotype_files/genotype/json + env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \ + GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \ + etc/default_settings.py -c -m unittest discover -v diff --git a/README.md b/README.md index 46264252..cd35defb 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ [](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [](http://joss.theoj.org/papers/10.21105/joss.00025) +[](https://github.com/genenetwork/genenetwork2/actions) # GeneNetwork @@ -42,9 +43,17 @@ Also mariadb and redis need to be running, see ## Testing To have tests pass, the redis and mariadb instance should be running, because of -asserts sprinkled in the code base(these will be removed in due time). +asserts sprinkled in the code base. + +Right now, the only tests running in CI are unittests. Please make +sure the existing unittests are green when submitting a PR. + +See +[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org) +for more details. #### Mechanical Rob + We are building 'Mechanical Rob' automated testing using Python [requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests) which can be run with: diff --git a/doc/docker-container.org b/doc/docker-container.org new file mode 100644 index 00000000..3c9864c5 --- /dev/null +++ b/doc/docker-container.org @@ -0,0 +1,86 @@ +#+TITLE: Genenetwork2 Dockerized + +* Table of Contents :TOC: +- [[#introduction][Introduction]] +- [[#creating-the-docker-images][Creating the Docker Images]] +- [[#pushing-to-dockerhub][Pushing to DockerHub]] + +* Introduction + +The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github +Actions]]. As such, it's important to have a way to run tests using +facilities provided by GUIX in a reproducible way. This project +leverages GUIX to generate a docker container from which the unittests +are ran from. + +Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This +document will not get into that. It's assumed that you have a working +dockec setup. + +The rest of this document outlines how the docker container used in +the CI builds were created. + +* Creating the Docker Images + +First create the image by running: + +#+begin_src sh +# For the Python 2 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack -f docker --no-grafts \ + -S /usr/bin=/bin -S /etc/profile=/etc/profile \ + -S /share/genenetwork2=/share/genenetwork2 \ + -S /share/javascript=/share/javascript \ + -S /lib=/lib \ + -S /usr/gn2-profile=/ \ + coreutils bash genenetwork2 + +# For the Python 3 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack -f docker --no-grafts \ + -S /usr/bin=/bin -S /etc/profile=/etc/profile \ + -S /share/genenetwork2=/share/genenetwork2 \ + -S /share/javascript=/share/javascript \ + -S /lib=/lib \ + -S /usr/gn2-profile=/ \ + coreutils bash python3-genenetwork2 + #+end_src + +The output will look something similar to: + +: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz + +Load the docker image by running: + +: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz + +Results look something similar to: + +#+begin_export ascii +a93f52b7f565: Loading layer 3.174GB/3.174GB +Loaded image: coreutils-genenetwork2:latest +#+end_export + +Assuming you have a docker instance running, you could always run +commands in it e.g: + +: docker run "coreutils-genenetwork2:latest" python --version + + +* Pushing to DockerHub + +We use DockerHub to store the docker images from which we use on our +CI environment using Github Actions. + +To push to dockerhub, first get the image name by running =docker +images=. Push to dockerhub using a command similar to: + +: docker push bonfacekilz/python2-genenetwork2:latest + +Right now, we have 2 images on DockerHub: + +- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2: + Contains the python2 version of gn2. Don't use this. Please use the + python3 image! +- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2: + Contains the python3 version of gn2. diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py index d070dab9..d4c3b1ad 100644 --- a/test/requests/main_web_functionality.py +++ b/test/requests/main_web_functionality.py @@ -20,7 +20,7 @@ def check_search_page(host): , search_terms_or="" , search_terms_and="MEAN=(15 16) LRS=(23 46)") result = requests.get(host+"/search", params=data) - found = result.text.find("records are shown below") + found = result.text.find("records were found") assert(found >= 0) assert(result.status_code == 200) print("OK") diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 94780a5d..dd7f5051 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_key_mrna(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_key_pheno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase): redis_mock.set.assert_called_once_with( "dataset_structure", '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" db_mock.db.execute.assert_called_with( ("SELECT InfoFiles.GN_AccesionId " + "FROM InfoFiles, PublishFreeze, InbredSet " + @@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_other_pheno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase): redis_mock.set.assert_called_once_with( "dataset_structure", '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" db_mock.db.execute.assert_called_with( ("SELECT PublishFreeze.Name " + "FROM PublishFreeze, InbredSet " + @@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_geno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py new file mode 100644 index 00000000..53b0d440 --- /dev/null +++ b/wqflask/tests/base/test_trait.py @@ -0,0 +1,101 @@ +# -*- coding: utf-8 -*- +"""Tests wqflask/base/trait.py""" +import unittest +import mock + +from base.trait import GeneralTrait +from base.trait import retrieve_trait_info + + +class TestResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return "[1, 2, 3, 4]" + + +class TestNilResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return "{}" + + +class MockTrait(GeneralTrait): + @property + def wikidata_alias_fmt(self): + return "Mock alias" + + +class TestRetrieveTraitInfo(unittest.TestCase): + """Tests for 'retrieve_trait_info'""" + def test_retrieve_trait_info_with_empty_dataset(self): + """Test that an exception is raised when dataset is empty""" + with self.assertRaises(AssertionError): + retrieve_trait_info(trait=mock.MagicMock(), + dataset={}) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_with_empty_trait_info(self, + g_mock, + requests_mock): + """Empty trait info""" + requests_mock.return_value = TestNilResponse() + with self.assertRaises(KeyError): + retrieve_trait_info(trait=mock.MagicMock(), + dataset=mock.MagicMock()) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_with_non_empty_trait_info(self, + g_mock, + requests_mock): + """Test that attributes are set""" + mock_dataset = mock.MagicMock() + requests_mock.return_value = TestResponse() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset), + dataset=mock_dataset) + self.assertEqual(test_trait.a, 1) + self.assertEqual(test_trait.b, 2) + self.assertEqual(test_trait.c, 3) + self.assertEqual(test_trait.d, 4) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_utf8_parsing(self, + g_mock, + requests_mock): + """Test that utf-8 strings are parsed correctly""" + utf_8_string = "test_string" + mock_dataset = mock.MagicMock() + requests_mock.return_value = TestResponse() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + type(mock_dataset).type = 'Publish' + + mock_trait = MockTrait( + dataset=mock_dataset, + pre_publication_description=utf_8_string + ) + trait_attrs = { + "group_code": "test_code", + "pre_publication_description": "test_pre_pub", + "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。", + "post_publication_description": None, + "pubmed_id": None, + 'year': "2020", + "authors": "Jane Doe かいと", + } + for key, val in list(trait_attrs.items()): + setattr(mock_trait, key, val) + test_trait = retrieve_trait_info(trait=mock_trait, + dataset=mock_dataset) + self.assertEqual(test_trait.abbreviation, + "ファイルを画面毎に見て行くには、次のコマンドを使います。") + self.assertEqual(test_trait.authors, + "Jane Doe かいと") diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py new file mode 100644 index 00000000..99c74245 --- /dev/null +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -0,0 +1,193 @@ +"""Tests for authentication tools""" +import unittest +import mock + +from utility.authentication_tools import check_resource_availability +from utility.authentication_tools import add_new_resource + + +class TestResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return '["foo"]' + + +class TestUser: + """Mock user""" + @property + def user_id(self): + """Mockes user id. Used in Flask.g.user_session.user_id""" + return "Jane" + + +class TestUserSession: + """Mock user session""" + @property + def user_session(self): + """Mock user session. Mocks Flask.g.user_session object""" + return TestUser() + + +def mock_add_resource(resource_ob, update=False): + return resource_ob + + +class TestCheckResourceAvailability(unittest.TestCase): + """Test methods related to checking the resource availability""" + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + add_new_resource_mock.return_value = {"default_mask": 2} + self.assertEqual(check_resource_availability(test_dataset), 2) + + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_non_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + ['foo']) + + @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES', + "SUPERUSER") + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g', TestUserSession()) + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_of_super_user( + self, + resource_id_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability if the user is the super user""" + resource_id_mock.return_value = 1 + redis_mock.smembers.return_value = ["Jane"] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + "SUPERUSER") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_string_dataset(self): + """Test the resource availability if the dataset is a string""" + self.assertEqual(check_resource_availability("Test"), + "John Doe") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_temp(self): + """Test the resource availability if the dataset is a string""" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Temp") + self.assertEqual(check_resource_availability(test_dataset), + "John Doe") + + +class TestAddNewResource(unittest.TestCase): + """Test cases for add_new_resource method""" + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_publish_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Publish") + type(test_dataset).id = mock.PropertyMock(return_value=10) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Test_None", + "data": { + "dataset": 10, + "trait": None + }, + "type": "dataset-publish" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_geno_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'geno'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="Geno") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-geno" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_other_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is not 'geno' or 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="other") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-probeset" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py new file mode 100644 index 00000000..16b50771 --- /dev/null +++ b/wqflask/tests/utility/test_hmac.py @@ -0,0 +1,39 @@ +# -*- coding: utf-8 -*- +"""Test hmac utility functions""" + +import unittest +import mock + +from utility.hmac import data_hmac +from utility.hmac import url_for_hmac +from utility.hmac import hmac_creation + + +class TestHmacUtil(unittest.TestCase): + """Test Utility method for hmac creation""" + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_hmac_creation(self): + """Test hmac creation with a utf-8 string""" + self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_data_hmac(self): + """Test data_hmac fn with a utf-8 string""" + self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_plain_url(self, mock_url): + """Test url_for_hmac without params""" + mock_url.return_value = "https://mock_url.com/ファイ/" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_param_in_url(self, mock_url): + """Test url_for_hmac with params""" + mock_url.return_value = "https://mock_url.com/?ファイ=1" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79") diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 3553b92b..239b08e3 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,4 +1,6 @@ from __future__ import absolute_import, print_function, division +import logging +from flask import Flask, g, redirect, url_for import json import requests @@ -9,33 +11,31 @@ from utility import hmac from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource Redis = get_redis_conn() -from flask import Flask, g, redirect, url_for -import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) + def check_resource_availability(dataset, trait_id=None): - #At least for now assume temporary entered traits are accessible - if type(dataset) == str: - return webqtlConfig.DEFAULT_PRIVILEGES - if dataset.type == "Temp": + # At least for now assume temporary entered traits are accessible + if type(dataset) == str or dataset.type == "Temp": return webqtlConfig.DEFAULT_PRIVILEGES resource_id = get_resource_id(dataset, trait_id) - if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno + if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno resource_info = get_resource_info(resource_id) - if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges + if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges resource_info = add_new_resource(dataset, trait_id) - #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy if g.user_session.user_id in Redis.smembers("super_users"): - return webqtlConfig.SUPER_PRIVILEGES + return webqtlConfig.SUPER_PRIVILEGES response = None - the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/available?resource={}&user={}".format( + resource_id, g.user_session.user_id) try: response = json.loads(requests.get(the_url).content) except: @@ -43,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None): return response + def add_new_resource(dataset, trait_id=None): resource_ob = { - 'owner_id' : "none", # webqtlConfig.DEFAULT_OWNER_ID, + 'owner_id': "none", # webqtlConfig.DEFAULT_OWNER_ID, 'default_mask': webqtlConfig.DEFAULT_PRIVILEGES, - 'group_masks' : {} + 'group_masks': {} } if dataset.type == "Publish": resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id) resource_ob['data'] = { 'dataset': dataset.id, - 'trait' : trait_id + 'trait': trait_id } resource_ob['type'] = 'dataset-publish' elif dataset.type == "Geno": @@ -74,15 +75,19 @@ def add_new_resource(dataset, trait_id=None): return resource_info + def get_group_code(dataset): - results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone() + results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format( + dataset.group.name)).fetchone() if results[0]: return results[0] else: return "" + def check_admin(resource_id=None): - the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/available?resource={}&user={}".format( + resource_id, g.user_session.user_id) try: response = json.loads(requests.get(the_url).content)['admin'] except: @@ -96,6 +101,7 @@ def check_admin(resource_id=None): else: return "not-admin" + def check_owner(dataset=None, trait_id=None, resource_id=None): if resource_id: resource_info = get_resource_info(resource_id) @@ -110,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None): return False + def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): if not resource_id: if dataset.type == "Temp": diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index b08be97e..fd75803e 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -7,11 +7,11 @@ from flask import url_for from wqflask import app + def hmac_creation(stringy): """Helper function to create the actual hmac""" secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(secret, stringy, hashlib.sha1) hm = hmaced.hexdigest() # ZS: Leaving the below comment here to ask Pjotr about @@ -20,10 +20,12 @@ def hmac_creation(stringy): hm = hm[:20] return hm + def data_hmac(stringy): - """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with""" + """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with""" return stringy + ":" + hmac_creation(stringy) + def url_for_hmac(endpoint, **values): """Like url_for but adds an hmac at the end to insure the url hasn't been tampered with""" @@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values): combiner = "?" return url + combiner + "hm=" + hm + app.jinja_env.globals.update(url_for_hmac=url_for_hmac, - data_hmac=data_hmac) \ No newline at end of file + data_hmac=data_hmac) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 81ba04ea..ef02268e 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -4,23 +4,21 @@ import uuid import simplejson as json import datetime -import redis # used for collections - -import logging - -from flask import (render_template, flash) - -from utility import hmac +import redis # used for collections +from utility.hmac import hmac_creation from utility.logger import getLogger logger = getLogger(__name__) + def get_redis_conn(): Redis = redis.StrictRedis(port=6379) return Redis + Redis = get_redis_conn() + def is_redis_available(): try: Redis.ping() @@ -28,6 +26,7 @@ def is_redis_available(): return False return True + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -38,6 +37,7 @@ def get_user_id(column_name, column_value): return None + def get_user_by_unique_column(column_name, column_value): item_details = None @@ -52,9 +52,11 @@ def get_user_by_unique_column(column_name, column_value): return item_details + def get_users_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_users = [] @@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, column_value): return matched_users -# def search_users_by_unique_column(column_name, column_value): def set_user_attribute(user_id, column_name, column_value): user_info = json.loads(Redis.hget("users", user_id)) @@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value): Redis.hset("users", user_id, json.dumps(user_info)) + def get_user_collections(user_id): collections = None collections = Redis.hget("collections", user_id) @@ -91,22 +93,27 @@ def get_user_collections(user_id): else: return [] + def save_user(user, user_id): Redis.hset("users", user_id, json.dumps(user)) + def save_collections(user_id, collections_ob): Redis.hset("collections", user_id, collections_ob) + def save_verification_code(user_email, code): Redis.hset("verification_codes", code, user_email) + def check_verification_code(code): email_address = None user_details = None email_address = Redis.hget("verification_codes", code) if email_address: - user_details = get_user_by_unique_column('email_address', email_address) + user_details = get_user_by_unique_column( + 'email_address', email_address) if user_details: return user_details else: @@ -114,10 +121,12 @@ def check_verification_code(code): else: return None + def get_user_groups(user_id): - #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups - admin_group_ids = [] #ZS: Group IDs where user is an admin - user_group_ids = [] #ZS: Group IDs where user is a regular user + # ZS: Get the groups where a user is an admin or a member and + # return lists corresponding to those two sets of groups + admin_group_ids = [] # ZS: Group IDs where user is an admin + user_group_ids = [] # ZS: Group IDs where user is a regular user groups_list = Redis.hgetall("groups") for key in groups_list: try: @@ -142,6 +151,7 @@ def get_user_groups(user_id): return admin_groups, user_groups + def get_group_info(group_id): group_json = Redis.hget("groups", group_id) group_info = None @@ -150,6 +160,7 @@ def get_group_info(group_id): return group_info + def get_group_by_unique_column(column_name, column_value): """ Get group by column; not sure if there's a faster way to do this """ @@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value): all_group_list = Redis.hgetall("groups") for key in all_group_list: group_info = json.loads(all_group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -167,9 +179,11 @@ def get_group_by_unique_column(column_name, column_value): return matched_groups + def get_groups_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_groups = [] @@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_name != "group_id": for key in group_list: group_info = json.loads(group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value): return matched_groups -def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): + +def create_group(admin_user_ids, member_user_ids=[], + group_name="Default Group Name"): group_id = str(uuid.uuid4()) new_group = { - "id" : group_id, + "id": group_id, "admins": admin_user_ids, - "members" : member_user_ids, - "name" : group_name, + "members": member_user_ids, + "name": group_name, "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') } @@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro return new_group + def delete_group(user_id, group_id): - #ZS: If user is an admin of a group, remove it from the groups hash + # ZS: If user is an admin of a group, remove it from the groups hash group_info = get_group_info(group_id) if user_id in group_info["admins"]: Redis.hdel("groups", group_id) @@ -214,9 +232,15 @@ def delete_group(user_id, group_id): else: None -def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set + +# ZS "admins" is just to indicate whether the users should be added to +# the groups admins or regular users set +def add_users_to_group(user_id, group_id, user_emails=[], admins=False): group_info = get_group_info(group_id) - if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are + # ZS: Just to make sure that the user is an admin for the group, + # even though they shouldn't be able to reach this point unless + # they are + if user_id in group_info["admins"]: if admins: group_users = set(group_info["admins"]) else: @@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS else: group_info["members"] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) return group_info else: return None -def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins + +# ZS: User type is because I assume admins can remove other admins +def remove_users_from_group(user_id, + users_to_remove_ids, + group_id, + user_type="members"): group_info = get_group_info(group_id) if user_id in group_info["admins"]: users_to_remove_set = set(users_to_remove_ids) - if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less + # ZS: Make sure an admin can't remove themselves from a group, + # since I imagine we don't want groups to be able to become + # admin-less + if user_type == "admins" and user_id in users_to_remove_set: users_to_remove_set.remove(user_id) group_users = set(group_info[user_type]) group_users -= users_to_remove_set group_info[user_type] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) + def change_group_name(user_id, group_id, new_name): group_info = get_group_info(group_id) if user_id in group_info["admins"]: @@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name): else: return None + def get_resources(): resource_list = Redis.hgetall("resources") return resource_list + def get_resource_id(dataset, trait_id=None): resource_id = False if dataset.type == "Publish": if trait_id: - resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) + resource_id = hmac_creation("{}:{}:{}".format( + 'dataset-publish', dataset.id, trait_id)) elif dataset.type == "ProbeSet": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-probeset', dataset.id)) elif dataset.type == "Geno": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-geno', dataset.id)) return resource_id + def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) if resource_info: @@ -282,17 +323,23 @@ def get_resource_info(resource_id): else: return None + def add_resource(resource_info, update=True): if 'trait' in resource_info['data']: - resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) + resource_id = hmac_creation('{}:{}:{}'.format( + str(resource_info['type']), str( + resource_info['data']['dataset']), + str(resource_info['data']['trait']))) else: - resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) + resource_id = hmac_creation('{}:{}'.format( + str(resource_info['type']), str(resource_info['data']['dataset']))) if update or not Redis.hexists("resources", resource_id): Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info + def add_access_mask(resource_id, group_id, access_mask): the_resource = get_resource_info(resource_id) the_resource['group_masks'][group_id] = access_mask @@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask): return the_resource + def change_resource_owner(resource_id, new_owner_id): - the_resource= get_resource_info(resource_id) + the_resource = get_resource_info(resource_id) the_resource['owner_id'] = new_owner_id Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file + Redis.hset("resources", resource_id, json.dumps(the_resource)) |