CCMS workflow tool tests

.github/workflows/workflow-tools.yml

@@ -0,0 +1,31 @@
+name: workflow-tools
+
+on:
+  pull_request:
+    branches:
+      master
+  push:
+    branches:
+      master
+  schedule:
+    - cron:  '1 12 * * *'
+
+jobs:
+  workflow-tools-test:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        submodules: recursive
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Test with nose2
+      run: |
+        pip install nose2
+        cd tool_integration && nose2 -v

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "GNPS_Workflows"]
 	path = GNPS_Workflows
 	url = https://github.com/CCMS-UCSD/GNPS_Workflows.git
+[submodule "CCMS-Workflow-Tools"]
+	path = CCMS-Workflow-Tools
+	url = [email protected]:CCMS-UCSD/CCMS-Workflow-Tools.git

tool_integration/test_tools.py

@@ -0,0 +1,37 @@
+    I A  bin/test_tools.py (Modified)(python)  def test_all_submodule_tools():                                                                                                                     Row 34   Col 35   3:15  Ctrl-K H for help
+#!/usr/bin/python
+
+import argparse
+import configparser
+import os
+import sys
+
+# set up script constants
+DEFAULT_SUBMODULE = "CCMS-Workflow-Tools"
+
+def test_all_submodule_tools():
+    # get command line arguments
+    argument_parser = argparse.ArgumentParser()
+    argument_parser.add_argument("-s", "--submodule", help="Name of submodule repository to search for test configurations to run.")
+    arguments = argument_parser.parse_args(sys.argv[1:])
+    # if argument submodule is not specified, use the default
+    submodule = arguments.submodule
+    if not submodule:
+        submodule = DEFAULT_SUBMODULE
+    # argument submodule should be present directly under working directory
+    assert(os.path.isdir(submodule), "Specified submodule [" + submodule + "] could not be found in this test environment.")
+    # check all top-level directories of the argument submodule
+    directories = os.listdir(submodule)
+    for directory in directories:
+        if os.path.isdir(directory):
+            # look for a "test" subdirectory under this directory
+            test_directory = os.path.join(directory, "test")
+            if os.path.isdir(test_directory):
+                # look for a "test.properties" file under this test subdirectory
+                test_properties_file = os.path.join(test_directory, "test.properties")
+                if os.path.isfile(test_properties_file):
+                    configuration = configparser.RawConfigParser()
+                    configuration.read(test_properties_file)
+                    test_parameters = dict(configuration.items("test properties"))
+                    test_command = test_parameters["test_command"]
+                    print("Test command = [" + test_command + "]")