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| -rw-r--r-- | README.md | 34 | ||||
| -rw-r--r-- | doc/testing.org | 66 | ||||
| -rw-r--r-- | test/unittest/__init__.py | 0 | ||||
| -rw-r--r-- | test/unittest/base/__init__.py | 0 | ||||
| -rw-r--r-- | test/unittest/base/test_general_object.py | 21 |
5 files changed, 77 insertions, 44 deletions
@@ -40,9 +40,13 @@ Also Mysql and Elasticsearch 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). + +#### Mechanical Rob We are building 'Mechanical Rob' automated testing using Python -[requests](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) -which can be run with something like +[requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests) +which can be run with: ```sh env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003 @@ -54,6 +58,32 @@ and executes test-website.py in a Python interpreter. The -a switch says to run all tests and the URL points to the running GN2 http server. +#### Unit tests + +To run unittests, first `cd` into the genenetwork2 directory: + +```sh +# You can use the coverage tool to run the tests +# You could omit the -v which makes the output verbose +runcmd coverage run -m unittest discover -v + +# Alternatively, you could run the unittests using: +runpython -m unittest discover -v + +# To generate a report in wqflask/coverage_html_report/: +runcmd coverage html +``` + +The `runcmd` and `runpython` are shell aliases defined in the following way: + +```sh +alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 + +alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli" +``` + +Replace some of the env variables as per your use case. + ## Documentation User documentation can be found diff --git a/doc/testing.org b/doc/testing.org index 1d5cc8b8..d5ab117d 100644 --- a/doc/testing.org +++ b/doc/testing.org @@ -1,43 +1,67 @@ #+TITLE: Testing GN2 * Table of Contents :TOC: - - [[#introduction][Introduction]] - - [[#run-tests][Run tests]] - - [[#setup][Setup]] - - [[#running][Running]] +- [[#introduction][Introduction]] +- [[#run-tests][Run tests]] + - [[#setup][Setup]] + - [[#running][Running]] * Introduction -For integration testing we currently use the brilliant Ruby Mechanize -gem against the small database; a setup we call mechanical Rob because -it emulates someone clicking through the website and checking results. +For integration testing, we currently use [[https://github.com/genenetwork/genenetwork2/tree/testing/test/requests][Mechanica Rob]] against the +small [[https://github.com/genenetwork/genenetwork2/blob/testing/doc/database.org][database]]; a setup we call Mechanical Rob because it emulates +someone clicking through the website and checking results. -These scripts invoke calls to a running webserver and test the -response. If a page changes or is broken tests will break and we are -informed. In principle, Mechanical Rob is run before code merges are -committed to the main server. +These scripts invoke calls to a running webserver and test the response. +If a page changes or breaks, tests will fail. In principle, Mechanical +Rob runs before code merges get committed to the main server. -In the future we may move to Python mechanize - it'll be easy to mix -the Ruby and Python versions. +For unit tests, we use python's =unittest= framework. Coverage reports +get generated using [[https://coverage.readthedocs.io/en/coverage-5.2.1/][coverage.py]] which you could also use to run +unit tests. When adding new functionality, it is advisable to add +unit tests. * Run tests ** Setup -Mechanize is not yet included in Guix deployment. +Everything required for testing is already package with guix: +: ./pre-ins-env guix package -i genenetwork2 -p ~/opt/genenetwork2 ** Running -Run the tests from the root of the genenetwork2 source tree as, for -example, +Run the tests from the root of the genenetwork2 source tree as. Ensure +that Redis and Mariadb are running. -: ./bin/test-website http://localhost:5003/ (default) +To run Mechanical Rob: +: time env GN2_PROFILE=~/opt/genenetwork2 TMPDIR=~/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -c ~/projects/genenetwork2/test/requests/test-website.py -a http://localhost:5004 -If you are using the small deployment database you can use +Use these aliases for the following examples. -: ./bin/test-website --skip -n +#+begin_src sh +alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 -To run individual tests on localhost you can do +alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli" +#+end_src -: ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/" +You could use them in your =.bashrc= or =.zshrc= file. + +To run unit tests: + +: runpython -m unittest discover -v + +Or alternatively using the coverage tool: + +: runcmd coverage run -m unittest discover -v + +To generate a html coverage report in =wqflask/coverage_html_report/= + +: runcmd coverage html + +To output the report to =STDOUT=: + +: runcmd coverage report + +All the configs for running the coverage tool are in +=wqflask/.coveragerc= diff --git a/test/unittest/__init__.py b/test/unittest/__init__.py deleted file mode 100644 index e69de29b..00000000 --- a/test/unittest/__init__.py +++ /dev/null diff --git a/test/unittest/base/__init__.py b/test/unittest/base/__init__.py deleted file mode 100644 index e69de29b..00000000 --- a/test/unittest/base/__init__.py +++ /dev/null diff --git a/test/unittest/base/test_general_object.py b/test/unittest/base/test_general_object.py deleted file mode 100644 index 699cb079..00000000 --- a/test/unittest/base/test_general_object.py +++ /dev/null @@ -1,21 +0,0 @@ -import unittest - -from base.GeneralObject import GeneralObject - - -class TestGeneralObjectTests(unittest.TestCase): - """ - Test the GeneralObject base class - """ - - def test_object_contents(self): - """Test whether base contents are stored properly""" - test_obj = GeneralObject("a", "b", "c") - self.assertEqual("abc", ''.join(test_obj.contents)) - - def test_object_dict(self): - """Test whether the base class is printed properly""" - test_obj = GeneralObject("a", name="test", value=1) - self.assertEqual(str(test_obj), "value = 1\nname = test\n") - self.assertEqual( - repr(test_obj), "value = 1\nname = test\ncontents = ['a']\n") |