fix(travis): remove travis CI, replace with GH Actions

.github/workflows/ci.yaml

@@ -9,7 +9,6 @@ concurrency:
   group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
   cancel-in-progress: true
 
-
 jobs:
   Security:
     name: Security Pipeline
@@ -18,7 +17,15 @@ jobs:
        python-poetry: 'false'
     secrets: inherit
 
-  ci:
+  UnitTest:
+    name: Python Unit Test with Postgres
+    uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
+    with:
+       setup-script: 'tests/ci_setup.sh'
+       test-script: 'tests/ci_commands_script.sh'
+       python-version: '3.9'
+
+  ImageBuildAndPush:
     name: Build Image and Push
     uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
     secrets:

.github/workflows/wool.yaml

@@ -0,0 +1,15 @@
+on:
+  pull_request
+
+name: Wool
+
+jobs:
+  runWool:
+    name: Run black
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+
+    - uses: uc-cdis/wool@master
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -56,3 +56,52 @@ see the README in that folder for more details.
 
 ## Submitter ID
 Sheepdog requires the `submitter_id` to be unique per node per project. It means that, the `submitter_id` of all `case` nodes must be unique per project. This constraint was technically enforced by the unique index of `(project_id, submitter_id)` in every node table.
+
+## Local Test Run Using CI Scripts
+
+If you want to locally replicate what GH Actions is doing more closely, follow
+these steps. 
+
+Ensure you've run `poetry install`. 
+
+Ensure you have Postgresql 13 set up and running.
+
+Ensure there is a postgres user `postgres` *and* `test` setup with password `test`:
+
+```
+CREATE USER postgres WITH PASSWORD 'test';
+```
+
+Then run:
+
+```bash
+bash tests/ci_setup.sh
+```
+
+If the above fails due to postgres errors, your postgresql setup may need some 
+fixing, it should finish with the following:
+
+```
+Setting up test database
+Dropping old test data
+WARNING:root:Unable to drop test data:(psycopg2.errors.InvalidCatalogName) database "sheepdog_automated_test" does not exist
+
+[SQL: DROP DATABASE "sheepdog_automated_test"]
+(Background on this error at: http://sqlalche.me/e/13/f405)
+Creating tables in test database
+Creating indexes
+writing RSA key
+```
+
+The WARNING will show up the first time you run this, it's safe to ignore.
+
+That sets up the database so if you run into postgres errors, you'll want to 
+double check your postgres setup.
+
+After that you can run unit tests with:
+
+```bash
+bash tests/ci_commands_script.sh
+```
+
+> You can see more detailed information on local dev setup in the docs/local_dev_environment.md

bin/setup_psqlgraph.py

@@ -195,7 +195,6 @@ def create_indexes(host, port, user, password, database, use_ssl=False):
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "--host", type=str, action="store", default="localhost", help="psql-server host"

tests/ci_commands_script.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+# since this whole thing is run as a bash {{this script}}, only the last pytest
+# command controls the exit code. We actually want to exit early if something fails
+set -e
+
+# datadict and datadictwithobjid tests must run separately to allow
+# loading different datamodels
+poetry run pytest -vv --cov=sheepdog --cov-report xml tests/integration/datadict
+poetry run pytest -vv --cov=sheepdog --cov-report xml --cov-append tests/integration/datadictwithobjid
+poetry run pytest -vv --cov=sheepdog --cov-report xml --cov-append tests/unit

tests/ci_setup.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+poetry run python bin/setup_test_database.py
+mkdir -p tests/integration/resources/keys
+cd tests/integration/resources/keys
+openssl genrsa -out test_private_key.pem 2048
+openssl rsa -in test_private_key.pem -pubout -out test_public_key.pem
+cd -

tests/integration/README.md

@@ -0,0 +1,10 @@
+TODO: Why are we integration testing alongside unit tests like this? We need to migrate
+      these tests elsewhere b/c it's not really integration testing if we're
+      configuring postgres exactly the way it expects in the CI running this. 
+      Since this CI setup is completely separate from how we run postgres in 
+      production, most of these tests are pointless.
+
+      As of 13 SEP 23 I'm ripping out some of this to enable the migration 
+      to Github Actions from Travis CI.
+
+      - Alex

tests/integration/datadict/test_ssl_and_isolation_level.py

@@ -1,5 +1,5 @@
 """
-Copy of a few functional tests in order to test that SSL and isolation level
+Copy of a few functional tests in order to test that isolation level
 settings work.
 """
 
@@ -18,28 +18,24 @@
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
     do_test_post_example_entities_together(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
     do_test_delete_entity(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
     do_test_submit_valid_tsv(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_export_all_node_types(
     client, pg_driver, cgci_blgsp, submitter, require_index_exists_off

tests/integration/datadictwithobjid/test_ssl_and_isolation_level.py

@@ -1,5 +1,5 @@
 """
-Copy of a few functional tests in order to test that SSL and isolation level
+Copy of a few functional tests in order to test that isolation level
 settings work.
 """
 
@@ -20,28 +20,24 @@
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
     do_test_post_example_entities_together(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
     do_test_delete_entity(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
     do_test_submit_valid_tsv(client, submitter)
 
 
 @pytest.mark.ssl
-@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
 @pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
 def test_export_all_node_types(
     client, pg_driver, cgci_blgsp, submitter, require_index_exists_off