Merge pull request #28 from aanil/add_tests

Fix existing, add more tests and make them run with Github actions

.github/workflows/run_tests.yml

@@ -0,0 +1,25 @@
+name: Run tests on push
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          cd $GITHUB_WORKSPACE
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r tests/requirements-test.txt
+          pip install pytest pytest-cov
+      - name: Test with pytest
+        run: |
+          python -m pytest --cov=daily_read tests

daily_read/__main__.py

@@ -52,17 +52,6 @@
 log = logging.getLogger(__name__)
 
 
-STATUS_PRIORITY = {
-    1: "Samples Received",
-    2: "Reception Control finished",
-    3: "Library QC finished",
-    4: "All Samples Sequenced",
-    5: "All Raw data Delivered",
-}
-
-STATUS_PRIORITY_REV = {v: k for k, v in STATUS_PRIORITY.items()}
-
-
 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))
 def daily_read_cli():
     pass
@@ -98,12 +87,12 @@ def generate_all(upload=False, develop=False):
             nr_orderers += 1
         if nr_orderers > 4 and develop:
             break
-    modified_orders = op.process_orders(STATUS_PRIORITY_REV)
+    modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
     daily_rep = daily_read.daily_report.DailyReport()
 
     for owner in modified_orders:
         if upload:
-            report = daily_rep.populate_and_write_report(owner, modified_orders[owner], STATUS_PRIORITY)
+            report = daily_rep.populate_and_write_report(owner, modified_orders[owner], config_values.STATUS_PRIORITY)
             # Publish reports
             for status in modified_orders[owner]["projects"].keys():
                 for project in modified_orders[owner]["projects"][status]:
@@ -118,7 +107,7 @@ def generate_all(upload=False, develop=False):
             report = daily_rep.populate_and_write_report(
                 owner,
                 modified_orders[owner],
-                STATUS_PRIORITY,
+                config_values.STATUS_PRIORITY,
                 out_dir=config_values.REPORTS_LOCATION,
             )
 
@@ -165,12 +154,12 @@ def generate_single(project, include_older=False):
         sys.exit(1)
 
     op.get_orders(orderer=orderer)
-    filtered_orders = op.process_orders(STATUS_PRIORITY_REV)
+    filtered_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
     daily_rep = daily_read.daily_report.DailyReport()
 
     for owner, owner_orders in filtered_orders.items():
         _ = daily_rep.populate_and_write_report(
-            owner, owner_orders, STATUS_PRIORITY, out_dir=config_values.REPORTS_LOCATION
+            owner, owner_orders, config_values.STATUS_PRIORITY, out_dir=config_values.REPORTS_LOCATION
         )
 
     log.info(f"Wrote report to {config_values.REPORTS_LOCATION}")

daily_read/config.py

@@ -16,3 +16,12 @@ def __init__(self):
         self.FETCH_FROM_NGIS = os.getenv("DAILY_READ_FETCH_FROM_NGIS")
         self.FETCH_FROM_SNPSEQ = os.getenv("DAILY_READ_FETCH_FROM_SNPSEQ")
         self.FETCH_FROM_UGC = os.getenv("DAILY_READ_FETCH_FROM_UGC")
+        self.STATUS_PRIORITY = {
+            0: "None",
+            1: "Samples Received",
+            2: "Reception Control finished",
+            3: "Library QC finished",
+            4: "All Samples Sequenced",
+            5: "All Raw data Delivered",
+        }
+        self.STATUS_PRIORITY_REV = {v: k for k, v in self.STATUS_PRIORITY.items()}

tests/.test.env

@@ -1,7 +1,10 @@
 # Test configuration variables
 
-DAILY_READ_ORDER_PORTAL_URL="https://orderportal.example.com"
+DAILY_READ_ORDER_PORTAL_URL="https://orderportal.example.com/"
+DAILY_READ_ORDER_PORTAL_API_KEY='fake12349183o18390301'
 DAILY_READ_DATA_LOCATION = "tests/test_data_location"
+DAILY_READ_REPORTS_LOCATION='tests/test_reports_location'
 DAILY_READ_FETCH_FROM_NGIS = true
 DAILY_READ_FETCH_FROM_SNPSEQ = true
 DAILY_READ_FETCH_FROM_UGC = true
+#DAILY_READ_LOG_LOCATION='tests/log_location'