Merge pull request #29 from aanil/add_tests

Add more tests for ngi_data and fix some bugs

daily_read/ngi_data.py

@@ -128,7 +128,7 @@ def save_data(self):
 
             abs_path = os.path.join(self.data_location, project_record.relative_path)
             if os.path.dirname(abs_path) != source_year_dir:  # This should really never happen
-                raise ValueError(f"Error with paths, dirname of {abs_path} should be {year_dir}")
+                raise ValueError(f"Error with paths, dirname of {abs_path} should be {source_year_dir}")
 
             with open(abs_path, mode="w") as fh:
                 log.debug(f"Writing data for {project_record.project_id} to {abs_path}")
@@ -188,7 +188,9 @@ def get_modified_or_new_projects(self):
                     internal_id,
                     internal_name,
                 ) = ProjectDataRecord.data_from_file(project_path)
-                project_record = ProjectDataRecord(project_path, orderer, project_dates, internal_id, internal_name)
+                project_record = ProjectDataRecord(
+                    project_path, orderer, project_dates, internal_id, internal_name, self.config.STATUS_PRIORITY_REV
+                )
             projects_list.append(project_record)
 
         return projects_list
@@ -218,23 +220,7 @@ class ProjectDataRecord(object):
     Raises ValueError if orderer is not present in data, if data is given
     """
 
-    dates_prio = {
-        "All Raw data Delivered": 5,
-        "All Samples Sequenced": 4,
-        "Library QC finished": 3,
-        "Reception Control finished": 2,
-        "Samples Received": 1,
-        "None": 0,
-    }
-
-    def __init__(
-        self,
-        relative_path,
-        orderer,
-        project_dates,
-        internal_id=None,
-        internal_name=None,
-    ):
+    def __init__(self, relative_path, orderer, project_dates, internal_id=None, internal_name=None, dates_prio=None):
         """relative_path: e.g. "NGIS/2023/NGI0002313.json" """
         node_year, file_name = os.path.split(relative_path)
         node, year = os.path.split(node_year)
@@ -268,7 +254,7 @@ def __init__(
 
             # If multiple statuses for the same date, choose the one with highest prio
             if len(latest_statuses) > 1:
-                self.status = sorted(latest_statuses, key=lambda s: self.dates_prio[s], reverse=True)[0]
+                self.status = sorted(latest_statuses, key=lambda s: dates_prio[s], reverse=True)[0]
             else:
                 self.status = latest_statuses[0]
         else:
@@ -326,6 +312,7 @@ def __init__(self, config):
         self.name = "NGI Stockholm"
         self.dirname = "NGIS"
         self.statusdb_session = statusdb.StatusDBSession(config)
+        self.dates_prio = config.STATUS_PRIORITY_REV
 
     def get_data(self, project_id=None, close_date=None):
         """Fetch data from Stockholm StatusDB.
@@ -350,7 +337,7 @@ def get_data(self, project_id=None, close_date=None):
                 internal_name = row.value["project_name"]
 
                 self.data[portal_id] = ProjectDataRecord(
-                    relative_path, orderer, project_dates, internal_id, internal_name
+                    relative_path, orderer, project_dates, internal_id, internal_name, self.dates_prio
                 )
 
         return self.data
@@ -364,7 +351,15 @@ def get_entry(self, project_id):
                 order_year = row.value["order_year"]
                 portal_id = row.value["portal_id"]
                 relative_path = f"{self.dirname}/{order_year}/{portal_id}.json"
-                self.data[portal_id] = ProjectDataRecord(relative_path, data=row.value)
+
+                project_dates = row.value["proj_dates"]
+                orderer = row.value["orderer"]
+                internal_id = row.value["project_id"]
+                internal_name = row.value["project_name"]
+
+                self.data[portal_id] = ProjectDataRecord(
+                    relative_path, orderer, project_dates, internal_id, internal_name, self.dates_prio
+                )
                 return
         raise ValueError(f"Project {project_id} not found in statusdb")
 
@@ -376,8 +371,8 @@ def __init__(self, config):
         self.name = "SNP&SEQ"
         self.dirname = "SNPSEQ"
 
-    def get_data(self, project_id=None):
-        pass
+    def get_data(self, project_id=None, close_date=None):
+        return {}
 
 
 class UGCProjectData(object):
@@ -387,5 +382,5 @@ def __init__(self, config):
         self.name = "Uppsala Genome Center"
         self.dirname = "UGC"
 
-    def get_data(self, project_id=None):
-        pass
+    def get_data(self, project_id=None, close_date=None):
+        return {}

tests/.test.env

@@ -7,4 +7,4 @@ 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'
+DAILY_READ_USERS_LIST_LOCATION=

tests/conftest.py

@@ -1,11 +1,13 @@
+import copy
+import couchdb
 import git
+import json
 import os
 import pytest
-import json
-from daily_read import ngi_data
+
 from datetime import date, timedelta
-import copy
 
+from daily_read import ngi_data, config
 
 dummy_order_open = {
     "orderer": "[email protected]",
@@ -25,8 +27,8 @@
         "2023-07-28": ["All Samples Sequenced"],
         "2023-07-29": ["All Raw data Delivered"],
     },
-    "internal_id": "P123456",
-    "internal_name": "D.Dummysson_23_01",
+    "internal_id": "P123455",
+    "internal_name": "D.Dummysson_23_02",
 }
 
 order_portal_resp_order_processing = {
@@ -159,7 +161,7 @@
     "fields": {
         "assigned_node": "Stockholm",
         "project_ngi_identifier": "P123455",
-        "project_ngi_name": "D.Dummysson_23_01",
+        "project_ngi_name": "D.Dummysson_23_02",
     },
 }
 
@@ -298,13 +300,15 @@ def data_repo_full(
 @pytest.fixture
 def mock_project_data_record():
     def _method(status):
+        config_values = config.Config()
         if status == "open":
             mock_record = ngi_data.ProjectDataRecord(
                 "NGIS/2023/NGI123456.json",
                 dummy_order_open["orderer"],
                 dummy_order_open["project_dates"],
                 dummy_order_open["internal_id"],
                 dummy_order_open["internal_name"],
+                config_values.STATUS_PRIORITY_REV,
             )
         if status == "closed":
             mock_record = ngi_data.ProjectDataRecord(
@@ -313,6 +317,7 @@ def _method(status):
                 dummy_order_closed["project_dates"],
                 dummy_order_closed["internal_id"],
                 dummy_order_closed["internal_name"],
+                config_values.STATUS_PRIORITY_REV,
             )
         if status == "open_with_report":
             mock_record = ngi_data.ProjectDataRecord(
@@ -321,6 +326,7 @@ def _method(status):
                 dummy_order_open["project_dates"],
                 dummy_order_open["internal_id"],
                 dummy_order_open["internal_name"],
+                config_values.STATUS_PRIORITY_REV,
             )
         return mock_record
 
@@ -357,3 +363,43 @@ def json(self):
         )
 
     return MockResponse(None, 404)
+
+
+@pytest.fixture
+def mocked_statusdb_conn_rows():
+    """To substitute return value for the daily_read.statusdb.StatusDBSession.rows method"""
+    row1 = couchdb.client.Row(
+        id="b77d4f",
+        key=["XXXX-XX-XX", "P123457"],
+        value={
+            "orderer": "[email protected]",
+            "portal_id": "NGI123457",
+            "order_year": "2023",
+            "project_id": "P123457",
+            "project_name": "D.Dummysson_23_03",
+            "proj_dates": {
+                "2023-06-15": ["Samples Received"],
+                "2023-06-28": ["Reception Control finished", "Library QC finished"],
+            },
+            "status": "Ongoing",
+        },
+    )
+    row2 = couchdb.client.Row(
+        id="b77d4g",
+        key=[(date.today() - timedelta(days=31)).strftime("%Y-%m-%d"), "P123458"],
+        value={
+            "orderer": "[email protected]",
+            "portal_id": "NGI123458",
+            "order_year": "2023",
+            "project_id": "P123458",
+            "project_name": "T.Dummysson_23_04",
+            "proj_dates": {
+                "2023-06-15": ["Samples Received"],
+                "2023-06-28": ["Reception Control finished", "Library QC finished"],
+                "2023-07-28": ["All Samples Sequenced"],
+                "2023-07-29": ["All Raw data Delivered"],
+            },
+            "status": "Closed",
+        },
+    )
+    return [row1, row2]

tests/test_daily_report.py

@@ -1,9 +1,9 @@
-import dotenv
 import datetime
+import dotenv
 import os
-from unittest import mock
-from conftest import mocked_requests_get
 
+from conftest import mocked_requests_get
+from unittest import mock
 
 from daily_read import daily_report, config, ngi_data, order_portal
 

tests/test_ngi_data.py

@@ -2,11 +2,14 @@
 
 import dotenv
 from unittest import mock
+import pytest
+import logging
 
 from daily_read import ngi_data, config
 
 dotenv.load_dotenv()
 
+LOGGER = logging.getLogger(__name__)
 
 ####################################################### TESTS #########################################################
 
@@ -129,12 +132,113 @@ def test_modified_or_new_tracked(data_repo_tracked):
     assert len(set(file_names)) == 0
 
 
+def test_get_unique_orderers(data_repo_full):
+    """Test getting unique orders in the project data from statusdb"""
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        data_master.get_data()
+        orderers = data_master.find_unique_orderers()
+        assert orderers == set(["[email protected]"])
+
+
+def test_user_list(data_repo_full, tmp_path, mocked_statusdb_conn_rows):
+    """Test getting and reading users from the user list url"""
+    config_values = config.Config()
+    temp_file = tmp_path / "test_file.txt"
+    temp_file.write_text("[email protected]\n[email protected]")
+    config_values.USERS_LIST_LOCATION = temp_file
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        assert not set(["[email protected]", "[email protected]"]) ^ set(data_master.user_list)
+
+        data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
+        data_master.get_data()
+        data_master.save_data()
+        orderers = data_master.find_unique_orderers()
+        assert orderers == set(["[email protected]", "[email protected]"])
+
+
+def test_save_data_to_disk(data_repo_full, mocked_statusdb_conn_rows):
+    """Test saving in git repo the data gotten from statusdb"""
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
+        data_master.get_data()
+        data_master.save_data()
+        assert os.path.exists(os.path.join(config_values.DATA_LOCATION, "NGIS/2023/NGI123457.json"))
+        assert os.path.exists(os.path.join(config_values.DATA_LOCATION, "NGIS/2023/NGI123458.json"))
+
+
+def test_get_data_with_project(data_repo_full, mocked_statusdb_conn_rows):
+    """Test getting data for a specific order"""
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
+        data_master.get_data("NGI123457")
+        assert len(data_master.data.keys()) == 1
+        assert "NGI123457" in data_master.data
+
+
+def test_get_data_with_project_unknown(data_repo_full, mocked_statusdb_conn_rows):
+    """Test error thrown when the order specified is not found in statusdb"""
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
+        with pytest.raises(ValueError, match="Project NGI123 not found in statusdb") as err:
+            data_master.get_data("NGI123")
+
+
+@mock.patch("daily_read.statusdb.StatusDBSession")
+def test_data_loc_not_abs(mock_status):
+    """Test error thrown when given data location is not an absolute path"""
+    config_values = config.Config()
+    config_values.DATA_LOCATION = "tests/test_data_location"
+    with pytest.raises(
+        ValueError, match=f"Data location is not an absolute path: {config_values.DATA_LOCATION}"
+    ) as err:
+        ngi_data.ProjectDataMaster(config_values)
+
+
+@mock.patch("daily_read.statusdb.StatusDBSession")
+def test_data_loc_not_dir(mock_status, tmp_path):
+    """Test error thrown when data location is not a directory"""
+    config_values = config.Config()
+    temp_file = tmp_path / "test_file.txt"
+    temp_file.write_text("test")
+    config_values.DATA_LOCATION = temp_file
+    with pytest.raises(
+        ValueError, match=f"Data Location exists but is not a directory: {config_values.DATA_LOCATION}"
+    ) as err:
+        ngi_data.ProjectDataMaster(config_values)
+
+
+def test_get_data_with_no_project_dates(data_repo_full, mocked_statusdb_conn_rows, caplog):
+    """Test log output when no project dates are found in statusdb for a specifi project"""
+    from copy import deepcopy
+
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+        data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
+        proj_no_dates = deepcopy(data_master.sources[0].statusdb_session.rows.return_value[0])
+        proj_no_dates.value["proj_dates"] = {}
+        proj_no_dates.value["portal_id"] = "NGI123459"
+        data_master.sources[0].statusdb_session.rows.return_value.append(proj_no_dates)
+        with caplog.at_level(logging.INFO):
+            data_master.get_data("NGI123459")
+            assert len(data_master.data.keys()) == 1
+            assert "NGI123459" in data_master.data
+            assert "No project dates found for NGI123459" in caplog.text
+
+
 # Planned tests #
 
 
 def test_getting_data():
-    # Test getting data
-    # When everything is ok
     # When some source fails
     # When all sources fails
     # When some source is not enabled
@@ -145,8 +249,6 @@ def test_getting_data():
     pass
 
 
-# Test saving data
-
 # Test add data for staging
 # If other things are added already
 # Test adding something that isn't changed