Merge pull request #31 from aanil/fix_git

Deal with aborted orders which were once in processing, also add codecov to see if it works
NationalGenomicsInfrastructure · Jan 17, 2024 · e4f0ded · e4f0ded
2 parents 69ef9e4 + 57e3f90
commit e4f0ded
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Showing 7 changed files with 132 additions and 15 deletions.
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -22,4 +22,8 @@ jobs:
           pip install pytest pytest-cov
       - name: Test with pytest
         run: |
-          python -m pytest --cov=daily_read tests
+          python -m pytest --cov=daily_read --cov-report=xml tests
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.md b/README.md
@@ -1,8 +1,10 @@
 # The NGI Daily Read
 
+[![codecov](https://codecov.io/gh/NationalGenomicsInfrastructure/DailyRead/graph/badge.svg?token=P3M4Y1N4SU)](https://codecov.io/gh/NationalGenomicsInfrastructure/DailyRead)
+
 A utility to generate and upload automatic progress reports for NGI Sweden.
 
-## Suggested logic
+## How it works
 
 - The script first fetches data from the appropriate NGI source, i.e. statusdb for Stockholm.
 - The data corresponding to each project will then be saved in a small data file (json, yaml or csv perhaps) on disk.
@@ -21,21 +23,21 @@ Also see diagram below:
 ![alt text](doc/figures/overview_dark.png#gh-dark-mode-only)
 ![alt text](doc/figures/overview_light.png#gh-light-mode-only)
 
-## Planned Usage (yet to be implemented)
+## Usage
 
 ```bash
 # Generate reports and save in a local git repository (location is given by configuration variable) and commit changes with a timestamp message
 daily_read generate all
 
-# Generate report for single orderer, need location specified, will not create git commit
-daily_read generate single <ordererID> <location>
+# Generate report for single orderer,
+daily_read generate single --project <OrderID>
 
 # Generate and upload
 daily_read generate all --upload
-daily_read generate single <orderer>
-
 ```
 
+To generate and upload reports for a single user(or a list of users), their name(s) can be entered in a text file and provided to the environment variable `DAILY_READ_USERS_LIST_LOCATION`.
+
 ## Configuration variables
 
 Configuration is dealt with via environment variables. Simplest way to set it up is to retrieve a `.env` file based on the `.env.example` provided in the repo. Environment variables which are not set have default variables in `daily_read/config.py`.

diff --git a/daily_read/ngi_data.py b/daily_read/ngi_data.py
@@ -190,9 +190,16 @@ def get_modified_or_new_projects(self):
                     project_dates,
                     internal_id,
                     internal_name,
+                    internal_proj_status,
                 ) = ProjectDataRecord.data_from_file(project_path)
                 project_record = ProjectDataRecord(
-                    project_path, orderer, project_dates, internal_id, internal_name, self.config.STATUS_PRIORITY_REV
+                    project_path,
+                    orderer,
+                    project_dates,
+                    internal_id,
+                    internal_name,
+                    self.config.STATUS_PRIORITY_REV,
+                    internal_proj_status,
                 )
             projects_list.append(project_record)
 
@@ -223,7 +230,16 @@ class ProjectDataRecord(object):
     Raises ValueError if orderer is not present in data, if data is given
     """
 
-    def __init__(self, relative_path, orderer, project_dates, internal_id=None, internal_name=None, dates_prio=None):
+    def __init__(
+        self,
+        relative_path,
+        orderer,
+        project_dates,
+        internal_id=None,
+        internal_name=None,
+        dates_prio=None,
+        internal_proj_status=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)
@@ -245,6 +261,7 @@ def __init__(self, relative_path, orderer, project_dates, internal_id=None, inte
         self.internal_name = internal_name
         self.events = []  # List of tuples (date_value, (date_status, <ProjectDataRecord>))
         self.status = None
+        self.internal_proj_status = internal_proj_status
 
         for date_value, date_statuses in project_dates.items():
             for date_status in date_statuses:
@@ -284,6 +301,7 @@ def data_for_file(self):
             "project_dates": self.project_dates,
             "internal_id": self.internal_id,
             "internal_name": self.internal_name,
+            "internal_proj_status": self.internal_proj_status,
         }
 
     def data_from_file(relative_path):
@@ -299,7 +317,11 @@ def data_from_file(relative_path):
         if "internal_name" in data:
             internal_name = data["internal_name"]
 
-        return data["orderer"], data["project_dates"], internal_id, internal_name
+        internal_proj_status = None
+        if "internal_proj_status" in data:
+            internal_proj_status = data["internal_proj_status"]
+
+        return data["orderer"], data["project_dates"], internal_id, internal_name, internal_proj_status
 
     def portal_id_from_path(path):
         """Class method to parse out project portal id (e.g. filename without extension) from given path"""
@@ -342,9 +364,16 @@ def get_data(self, project_id=None, close_date=None):
                 orderer = row.value["orderer"]
                 internal_id = row.value["project_id"]
                 internal_name = row.value["project_name"]
+                internal_proj_status = row.value["status"]
 
                 self.data[portal_id] = ProjectDataRecord(
-                    relative_path, orderer, project_dates, internal_id, internal_name, self.dates_prio
+                    relative_path,
+                    orderer,
+                    project_dates,
+                    internal_id,
+                    internal_name,
+                    self.dates_prio,
+                    internal_proj_status,
                 )
 
         return self.data
@@ -367,9 +396,16 @@ def get_entry(self, project_id):
                 orderer = row.value["orderer"]
                 internal_id = row.value["project_id"]
                 internal_name = row.value["project_name"]
+                internal_proj_status = row.value["status"]
 
                 self.data[portal_id] = ProjectDataRecord(
-                    relative_path, orderer, project_dates, internal_id, internal_name, self.dates_prio
+                    relative_path,
+                    orderer,
+                    project_dates,
+                    internal_id,
+                    internal_name,
+                    self.dates_prio,
+                    internal_proj_status,
                 )
                 return
         raise ValueError(f"Project {project_id} not found in statusdb")

diff --git a/daily_read/order_portal.py b/daily_read/order_portal.py
@@ -90,6 +90,10 @@ def process_orders(self, priority, closed_before_in_days=30):
                     delete_report = True
 
             proj_info = self.projects_data.data[order["identifier"]]
+
+            if proj_info.internal_proj_status in ["Aborted"]:
+                delete_report = True
+
             if order["reports"]:
                 prog_reports = [item for item in order["reports"] if item["name"] == "Project Progress"]
                 if prog_reports:

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -17,6 +17,7 @@
     },
     "internal_id": "P123456",
     "internal_name": "D.Dummysson_23_01",
+    "internal_proj_status": "Ongoing",
 }
 
 dummy_order_closed = {
@@ -29,6 +30,7 @@
     },
     "internal_id": "P123455",
     "internal_name": "D.Dummysson_23_02",
+    "internal_proj_status": "Ongoing",
 }
 
 order_portal_resp_order_processing = {
@@ -120,6 +122,26 @@
     },
 ]
 
+order_portal_resp_order_processing_to_aborted = copy.deepcopy(order_portal_resp_order_processing)
+order_portal_resp_order_processing_to_aborted["identifier"] = "NGI123461"
+order_portal_resp_order_processing_to_aborted["reports"] = [
+    {
+        "iuid": "c5ee943",
+        "name": "Project Progress",
+        "filename": "project_progress.html",
+        "status": "published",
+        "modified": "2024-01-15T15:09:18.732Z",
+        "links": {
+            "api": {"href": "https://orderportal.example.com/orders/api/v1/report/c5ee943"},
+            "file": {"href": "https://orderportal.example.com/orders/report/c5ee943"},
+        },
+    },
+]
+order_portal_resp_order_processing_to_aborted["status"] = "Rejected"
+order_portal_resp_order_processing_to_aborted["history"]["rejected"] = "2024-01-16"
+order_portal_resp_order_processing_to_aborted["fields"]["project_ngi_identifier"] = "P123461"
+order_portal_resp_order_processing_to_aborted["fields"]["project_ngi_name"] = "D.Dummysson_23_07"
+
 order_portal_resp_order_closed = {
     "identifier": "NGI123455",
     "title": "Test run with closed",
@@ -221,6 +243,7 @@ def data_repo_new_staged(data_repo):
         "NGIS/2023/staged_file2.json",
         "NGIS/2023/P123456.json",
         "NGIS/2023/P123453.json",
+        "NGIS/2023/P123461.json",
     ]
     _create_all_files(staged_files, data_repo.working_dir)
     data_repo.index.add(staged_files)
@@ -309,6 +332,7 @@ def _method(status):
                 dummy_order_open["internal_id"],
                 dummy_order_open["internal_name"],
                 config_values.STATUS_PRIORITY_REV,
+                dummy_order_open["internal_proj_status"],
             )
         if status == "closed":
             mock_record = ngi_data.ProjectDataRecord(
@@ -318,6 +342,7 @@ def _method(status):
                 dummy_order_closed["internal_id"],
                 dummy_order_closed["internal_name"],
                 config_values.STATUS_PRIORITY_REV,
+                dummy_order_closed["internal_proj_status"],
             )
         if status == "open_with_report":
             mock_record = ngi_data.ProjectDataRecord(
@@ -327,6 +352,17 @@ def _method(status):
                 dummy_order_open["internal_id"],
                 dummy_order_open["internal_name"],
                 config_values.STATUS_PRIORITY_REV,
+                dummy_order_open["internal_proj_status"],
+            )
+        if status == "open_to_aborted_with_report":
+            mock_record = ngi_data.ProjectDataRecord(
+                "NGIS/2023/NGI123461.json",
+                dummy_order_open["orderer"],
+                dummy_order_open["project_dates"],
+                "P123461",
+                "D.Dummysson_23_07",
+                config_values.STATUS_PRIORITY_REV,
+                "Aborted",
             )
         return mock_record
 
@@ -357,6 +393,7 @@ def json(self):
                     order_portal_resp_order_closed,
                     order_portal_resp_order_processing_mult_reports,
                     order_portal_resp_order_processing_single_report,
+                    order_portal_resp_order_processing_to_aborted,
                 ]
             },
             200,
@@ -412,7 +449,7 @@ def mocked_statusdb_conn_rows():
             "project_id": "P123460",
             "project_name": "D.Dummysson_23_06",
             "proj_dates": {},
-            "status": "Pending",
+            "status": "Reception control",
         },
     )
     return [row1, row2, row3]
diff --git a/tests/test_ngi_data.py b/tests/test_ngi_data.py
@@ -58,7 +58,7 @@ def test_modified_or_new(data_repo_full):
 
     modified_or_new = data_master.get_modified_or_new_projects()
     file_names = [project.relative_path for project in modified_or_new]
-    assert len(set(file_names)) == 11
+    assert len(set(file_names)) == 12
 
 
 def test_modified_or_new_untracked(data_repo_untracked):
@@ -84,7 +84,7 @@ def test_modified_or_new_staged(data_repo_new_staged):
 
     modified_or_new = data_master.get_modified_or_new_projects()
     file_names = [project.relative_path for project in modified_or_new]
-    assert len(set(file_names)) == 5
+    assert len(set(file_names)) == 6
     assert any("staged_file" in s for s in file_names)
 
 

diff --git a/tests/test_order_portal.py b/tests/test_order_portal.py
@@ -83,6 +83,40 @@ def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock
         )
 
 
+def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo_full, mock_project_data_record):
+    """Test getting, processing an open order with an existing Project progress report and uploading the report to the Order portal"""
+    orderer = "[email protected]"
+    order_id = "NGI123461"
+    config_values = config.Config()
+    with mock.patch("daily_read.statusdb.StatusDBSession"):
+        data_master = ngi_data.ProjectDataMaster(config_values)
+
+    data_master.data = {order_id: mock_project_data_record("open_to_aborted_with_report")}
+
+    op = order_portal.OrderPortal(config_values, data_master)
+    with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get):
+        op.get_orders(orderer=orderer)
+
+    assert op.all_orders[4]["identifier"] == order_id
+    modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
+
+    assert modified_orders[orderer]["delete_report_for"]["Library QC finished"][0] == data_master.data[order_id]
+    with mock.patch("daily_read.order_portal.requests.post") as mock_post:
+        mock_post.return_value.status_code = 200
+        op.upload_report_to_order_portal(
+            "", modified_orders[orderer]["delete_report_for"]["Library QC finished"][0], "review"
+        )
+        url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report/{op.all_orders[4]['reports'][0]['iuid']}"
+        indata = dict(
+            order=order_id,
+            name="Project Progress",
+            status="review",
+        )
+        mock_post.assert_called_once_with(
+            url, headers={"X-OrderPortal-API-key": config_values.ORDER_PORTAL_API_KEY}, json=indata
+        )
+
+
 def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record):
     """Test getting and processing an order closed within the timeframe of Project progress report deletion"""
     orderer = "[email protected]"