Fix workspace container tests

Tests pass locally but consistently fail on Github Actions.

* Downgraded ubuntu runner / kernel
* Made the tests themselves ensure that the services are available
rather than checking a possibly fragile log line.

Also moved them to a test directory rather than scripts.

Also also slightly modified the Docker file so slow steps are cached
before copying in code, which busts the cache.

.github/workflows/test.yml

@@ -19,7 +19,7 @@ on:
 jobs:
 
   workspace_container_tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v3
 
@@ -37,7 +37,7 @@ jobs:
       - name: Run tests
         shell: bash
         run: |
-          sh scripts/run_tests.sh
+          sh test/run_tests.sh
 
   workspace_deluxe_tests:
     runs-on: ubuntu-latest

Dockerfile

@@ -1,11 +1,13 @@
 FROM eclipse-temurin:11-jdk as build
 
-COPY . /tmp/workspace_deluxe
 WORKDIR /tmp
-RUN apt-get update -y && \
-    apt-get install -y ant git ca-certificates python3-sphinx && \
-    git clone https://github.com/kbase/jars && \
-    cd workspace_deluxe && \
+RUN apt update -y && \
+    apt install -y ant git ca-certificates python3-sphinx && \
+    git clone https://github.com/kbase/jars
+
+COPY . /tmp/workspace_deluxe
+
+RUN cd workspace_deluxe && \
     make docker_deps
 
 # updated/slimmed down version of what's in kbase/kb_jre

test/README.md

@@ -0,0 +1,2 @@
+This directory contains tests not part of the standard java suite. Currently it has a very small
+test suite that runs against the workspace in a docker container.

test/run_tests.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+#
+# Script to run the python workspace_container_test.py locally or on GitHub Actions.
+# Builds and mounts auth2, workspace, and mongo docker containers, and then calls
+# the python script.
+#
+# See .github/workflows/test.yml for GitHub Actions implementation.
+
+# build and start the containers
+docker compose up -d --build
+compose_up_exit_code=$?
+if [ $compose_up_exit_code -ne 0 ]; then
+    echo "Error: docker-compose up -d --build command failed with exit code $compose_up_exit_code."
+    exit $compose_up_exit_code
+fi
+
+# get the path to the current directory and add it to the python execution path
+current_dir="$( dirname -- "$( readlink -f -- "$0"; )"; )"
+PYTHONPATH="$current_dir":$PYTHONPATH python -m pytest test/workspace_container_test.py
+exit_code=$?
+
+docker compose down
+exit $exit_code

test/workspace_container_test.py

@@ -0,0 +1,116 @@
+from lib.biokbase.workspace.client import Workspace
+import pytest
+import requests
+import json
+import time
+
+""" workspace_container_test.py
+
+Very simple tests to ensure that local workspace and auth2 servers are functioning correctly.
+Requires the python libraries `pytest` and `requests` to be installed.
+
+Assumes that the workspace and auth2 are running locally on ports 8080 and 7058 respectively.
+
+Use the wrapper shell script, `run_tests.sh`, to create the necessary set up and run the tests:
+
+sh scripts/run_tests.sh
+
+"""
+
+WORKSPACE_VERSION = "0.14.3"
+
+AUTH_URL = "http://localhost:8080"
+WS_URL = "http://localhost:7058"
+USER_NAME = "some_dull_user"
+WS_NAME = "my_cool_new_workspace"
+WAIT_TIMES = [1, 2, 5, 10, 30]
+
+
+@pytest.fixture(scope="module")
+def ready():
+    wait_for_auth()
+    wait_for_ws()
+
+    yield
+
+def wait_for_auth():
+    print("waiting for auth service...")
+    for t in WAIT_TIMES:
+        try: 
+            res = requests.get(AUTH_URL)
+            res.raise_for_status()
+            return
+        except Exception as e:
+            print(f"Failed to connect to auth, waiting {t} sec and trying again:\n\t{e}")
+        time.sleep(t)
+    raise Exception(f"Couldn't connect to the auth after {len(WAIT_TIMES)} attempts")
+
+
+def wait_for_ws():
+    print("waiting for workspace service...")
+    ws = Workspace(WS_URL)
+    for t in WAIT_TIMES:
+        try:
+            ws.ver()
+            return
+        except Exception as e:
+            print(f"Failed to connect to workspace, waiting {t} sec and trying again:\n\t{e}")
+        time.sleep(t)
+    raise Exception(f"Couldn't connect to the workspace after {len(WAIT_TIMES)} attempts")
+
+
+def test_create_user_create_workspace(ready):
+    """create a user and then create a workspace for that user"""
+    token = create_auth2_user_token()
+    get_ws_version(token)
+    create_read_workspace(token)
+
+
+def create_auth2_user_token() -> str:
+    """create a user and generate a token for that user"""
+    # create a new user
+    user_json = json.dumps({"user": USER_NAME, "display": "Blah blah"})
+    response = requests.post(
+        AUTH_URL + "/testmode/api/V2/testmodeonly/user",
+        data=user_json,
+        headers={"content-type":"application/json"}
+    )
+    assert response.status_code == 200
+    user_data = response.json()
+    assert 'created' in user_data
+
+    # create the toke
+    token_json = json.dumps({ "user": USER_NAME, "type": "Login" })
+    response = requests.post(
+        AUTH_URL + "/testmode/api/V2/testmodeonly/token",
+        data=token_json,
+        headers={"content-type":"application/json"}
+    )
+    assert response.status_code == 200
+    token_data = response.json()
+    assert 'created' in token_data
+    assert 'token' in token_data
+    return token_data["token"]
+
+
+def get_ws_version(token: str) -> None:
+    """get the current workspace version"""
+    ws = Workspace(WS_URL, token=token)
+    assert ws.ver() == WORKSPACE_VERSION
+
+
+def create_read_workspace(token: str) -> None:
+    """create a new workspace and then get the workspace information"""
+    ws = Workspace(WS_URL, token=token)
+    new_ws = ws.create_workspace({'workspace': WS_NAME})
+    assert new_ws[1] == WS_NAME
+    assert new_ws[2] == USER_NAME
+    assert ws.get_workspace_info({ "id": new_ws[0] }) == new_ws
+
+
+def test_get_docs(ready) -> None:
+    """check that the workspace documentation can be accessed"""
+    response = requests.get(WS_URL + "/docs/")
+    assert response.status_code == 200
+    assert response.text.find("KBase Workspace Service Manual") != -1
+    assert response.text.find("KBase Workspace " + WORKSPACE_VERSION + " documentation") != -1