Bug/setup tests

.github/workflows/emap-setup-tests.yaml

@@ -0,0 +1,47 @@
+name: emap setup tests
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop, sk/waveform-dev ]
+  repository_dispatch:
+permissions:
+  contents: read
+  checks: write
+  id-token: write
+  pull-requests: read # needed by paths-filter
+jobs:
+  filter:
+    runs-on: ubuntu-latest
+    outputs:
+      emap-setup: ${{ steps.filter.outputs.emap-setup }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: |
+            emap-setup:
+              - '.github/**'
+              - 'emap-checker.xml'
+              - 'emap-setup/**'
+  emap-setup-tests:
+    needs: [filter]
+    runs-on: ubuntu-latest
+    env:
+       GITHUB_TOKEN: ${{ secrets.GH_PAT_READ_AND_COMMENT }}
+    if: needs.filter.outputs.emap-setup == 'true'
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: "pip"
+      - name: Install Python Dependencies
+        run: | 
+          python -m pip install -r emap-setup/requirements.txt
+      - name: Run tests
+        run: |
+          cd emap-setup
+          pytest  --cov=./ --cov-report=term

emap-setup/.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit = 
+    __init__.py
+    tests/*

emap-setup/emap_runner/setup/repos.py

@@ -1,4 +1,5 @@
 import git
+import os
 import shutil
 
 from pathlib import Path
@@ -118,6 +119,9 @@ def path(self) -> Path:
     @property
     def https_git_url(self) -> str:
         """Generate a https URL. e.g. https://github.com/../emap-setup.git"""
+        gh_token = os.environ.get('GITHUB_TOKEN', False)
+        if gh_token:
+            return f"https://{gh_token}@{self._base_git_url}/{self.name}"
         return f"https://{self._base_git_url}/{self.name}"
 
     @property

emap-setup/requirements.in

@@ -0,0 +1,7 @@
+pytest
+pytest-cov
+PyYAML
+gitpython
+black
+tqdm
+setuptools

emap-setup/requirements.txt

@@ -1,5 +1,57 @@
-pytest
-PyYAML
-gitpython
-black
-tqdm
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o requirements.txt
+black==25.9.0
+    # via -r requirements.in
+click==8.3.0
+    # via black
+coverage==7.10.7
+    # via pytest-cov
+exceptiongroup==1.3.0
+    # via pytest
+gitdb==4.0.12
+    # via gitpython
+gitpython==3.1.45
+    # via -r requirements.in
+iniconfig==2.1.0
+    # via pytest
+mypy-extensions==1.1.0
+    # via black
+packaging==25.0
+    # via
+    #   black
+    #   pytest
+pathspec==0.12.1
+    # via black
+platformdirs==4.4.0
+    # via black
+pluggy==1.6.0
+    # via
+    #   pytest
+    #   pytest-cov
+pygments==2.19.2
+    # via pytest
+pytest==8.4.2
+    # via
+    #   -r requirements.in
+    #   pytest-cov
+pytest-cov==7.0.0
+    # via -r requirements.in
+pytokens==0.1.10
+    # via black
+pyyaml==6.0.2
+    # via -r requirements.in
+setuptools==80.9.0
+    # via -r requirements.in
+smmap==5.0.2
+    # via gitdb
+tomli==2.2.1
+    # via
+    #   black
+    #   coverage
+    #   pytest
+tqdm==4.67.1
+    # via -r requirements.in
+typing-extensions==4.15.0
+    # via
+    #   black
+    #   exceptiongroup

emap-setup/tests/data/test-global-configuration-only-docs.yaml

@@ -6,7 +6,7 @@ EMAP_PROJECT_NAME:
   only_emap_setup
 
 repositories:
-  emap_documentation:
+  internal_emap_documentation:
     branch:  main
 # For testing outside the GAE, you can enable a fake UDS
 fake_uds:

emap-setup/tests/data/test-global-configuration-onlyhl7.yaml

@@ -6,8 +6,8 @@ EMAP_PROJECT_NAME:
   my_project_name
 
 repositories:
-  core:
-    branch:  main
+  emap:
+    branch:  develop
 
 rabbitmq:
   SPRING_RABBITMQ_HOST: rabbitmq
@@ -34,7 +34,7 @@ dates:
 common:
   UDS_JDBC_URL: jdbc:postgresql://host.docker.internal:5432/ids
 
-core:
+uds:
   UDS_SCHEMA: inform_schema
   UDS_USERNAME: someuser
   UDS_PASSWORD: redacted

emap-setup/tests/data/test-global-configuration.yaml

@@ -7,12 +7,11 @@ EMAP_PROJECT_NAME:
   my_project_name
 
 repositories:
-  InformDB:
-    branch:  develop
-  hl7-vitals:
-    branch:  main
-    repo_name: core
+  emap:
+    branch: develop
+
   hoover:
+    branch: main
 
 # Configuration data for the rabbitmq instance used by Spring in the pipeline
 
@@ -42,23 +41,11 @@ dates:
   start: 2020-06-04T00:00:00.00Z
   end:
 
-informdb:
-  common:
-    UDS_JDBC_URL: jdbc:postgresql://host.docker.internal:5432/ids
-  core:
-    UDS_SCHEMA: inform_schema
-    UDS_USERNAME: someuser
-    UDS_PASSWORD: redacted
-  OMOP-ETL:
-    UDS_SCHEMA: inform_schema
-    UDS_USERNAME: someuser_omop
-    UDS_PASSWORD: redacted_omop
-    UDS_DDL_AUTO: update
-    INFORM_INIT_MODE: always
-  hl7-vitals:
-    UDS_SCHEMA: inform_schema_for_branch
-    UDS_USERNAME: someuseraaa
-    UDS_PASSWORD: redactedaaa
+common:
+  UDS_JDBC_URL: jdbc:postgresql://host.docker.internal:5432/ids
+  UDS_SCHEMA: inform_schema
+  UDS_USERNAME: someuser
+  UDS_PASSWORD: redacted
 
 # For testing outside the GAE, you can enable a fake UDS
 fake_uds:

emap-setup/tests/test_runner.py

@@ -24,6 +24,9 @@
 config_path_all = Path(
     dirname(abspath(__file__)), "data", "test-global-configuration.yaml"
 )
+config_path_config_dir = Path(
+    dirname(abspath(__file__)), "data", "config"
+)
 
 
 @work_in_tmp_directory(to_copy=None)
@@ -36,14 +39,14 @@ def test_clone_then_clean_repos():
     runner.run()
 
     # Ensure that the cloned directory exists
-    assert exists("emap_documentation")
+    assert exists("internal_emap_documentation")
     assert exists("config")
 
     # and can be cleaned
     runner = EMAPRunner(args=parser.parse_args(["setup", "-c"]), config=config)
     runner.run()
 
-    assert not exists("emap_documentation")
+    assert not exists("internal_emap_documentation")
 
 
 @work_in_tmp_directory(to_copy=None)
@@ -58,7 +61,7 @@ def test_double_clone():
     runner = EMAPRunner(args=parser.parse_args(args), config=config)
     runner.run()
     # Make some un-pushed changes to newly cloned repo
-    file_to_keep = Path('emap_documentation/my_favourite_file.txt')
+    file_to_keep = Path('internal_emap_documentation/my_favourite_file.txt')
     with open(file_to_keep, 'w') as fh:
         fh.write("cheese")
 
@@ -148,6 +151,7 @@ def test_validation_source_arguments_set_correct_runner_attributes(args_list,
         (1, 1, False),
         (2, 1, True),
     ])
+@work_in_tmp_directory(to_copy=[config_path_config_dir])
 def test_validation_timeout(num_trues, timeout_seconds, expect_raises):
     parser = create_parser()
     args = parser.parse_args(["validation", "--use-waveform", "--timeout", str(timeout_seconds / 3600)])

emap-setup/tests/utils.py

@@ -1,7 +1,7 @@
 import os
 
 from shutil import rmtree, copy
-from distutils.dir_util import copy_tree
+import setuptools
 from pathlib import Path
 from tempfile import mkdtemp
 from functools import wraps
@@ -22,7 +22,7 @@ def wrapped_function(*args, **kwargs):
 
             for item in to_copy:
                 if Path(item).is_dir():
-                    copy_tree(item, tmpdir_path)
+                    setuptools.distutils.dir_util.copy_tree(item, tmpdir_path)
                 else:
                     copy(item, tmpdir_path)