feat(rm): pkg_resource (#3431)

### Changed

- Remove pkg_resource use for invoice and delivery report

cg/apps/invoice/render.py

@@ -1,8 +1,11 @@
 import datetime as dt
+from pathlib import Path
 
 from openpyxl import Workbook, load_workbook
 from openpyxl.styles import Border, Font, PatternFill, Side
-from pkg_resources import resource_filename
+
+from cg.constants import FileExtensions
+from cg.utils.files import get_project_root_dir
 
 
 def render_xlsx(data: dict) -> Workbook:
@@ -34,11 +37,17 @@ def render_xlsx(data: dict) -> Workbook:
             }]
         }
     """
-    pkg_dir = __name__.rpartition(".")[0]
+    project_root_dir = get_project_root_dir()
     sample_type = "pool" if data["pooled_samples"] else "sample"
     costcenter = data["cost_center"]
-    template_path = resource_filename(pkg_dir, f"templates/{costcenter}_{sample_type}_invoice.xlsx")
-    workbook = load_workbook(template_path)
+    template_path = Path(
+        project_root_dir,
+        "apps",
+        "invoice",
+        "templates",
+        f"{costcenter}_{sample_type}_invoice{FileExtensions.XLSX}",
+    )
+    workbook = load_workbook(template_path.as_posix())
     if data["pooled_samples"]:
         worksheet = workbook["Bilaga Prover"]
         worksheet["C1"] = costcenter.upper()

cg/constants/constants.py

@@ -223,6 +223,7 @@ class FileExtensions(StrEnum):
     TSV: str = ".tsv"
     TXT: str = ".txt"
     VCF: str = ".vcf"
+    XLSX: str = ".xlsx"
     XML: str = ".xml"
     YAML: str = ".yaml"
 

cg/constants/report.py

@@ -1,15 +1,17 @@
 """Delivery report constants."""
 
-from importlib.resources import files
 from pathlib import Path
 
 from cg.constants import DataDelivery
 from cg.constants.constants import CancerAnalysisType, FileExtensions, Workflow
 from cg.constants.subject import Sex
+from cg.utils.files import get_project_root_dir
+
+project_root_dir: Path = get_project_root_dir()
 
 DELIVERY_REPORT_FILE_NAME: str = f"delivery-report{FileExtensions.HTML}"
 SWEDAC_LOGO_PATH = Path(
-    files("cg"), "meta", "report", "templates", "static", "images", "SWEDAC_logo.png"
+    project_root_dir, "meta", "report", "templates", "static", "images", "SWEDAC_logo.png"
 )
 
 BALSAMIC_REPORT_ACCREDITED_PANELS: list[str] = ["gmsmyeloid"]

cg/resources/__init__.py

@@ -1,8 +1,9 @@
 from pathlib import Path
 
-import pkg_resources
-
 from cg.constants import FileExtensions
+from cg.utils.files import get_project_root_dir
+
+project_root_dir: Path = get_project_root_dir()
 
 RAREDISEASE_BUNDLE_FILENAMES: str = (
     Path("resources", "raredisease_bundle_filenames").with_suffix(FileExtensions.YAML).as_posix()
@@ -20,18 +21,10 @@
     Path("resources", "tomte_bundle_filenames").with_suffix(FileExtensions.YAML).as_posix()
 )
 
-RAREDISEASE_BUNDLE_FILENAMES_PATH = Path(
-    pkg_resources.resource_filename("cg", RAREDISEASE_BUNDLE_FILENAMES)
-)
+RAREDISEASE_BUNDLE_FILENAMES_PATH = Path(project_root_dir, RAREDISEASE_BUNDLE_FILENAMES)
 
-RNAFUSION_BUNDLE_FILENAMES_PATH: Path = Path(
-    pkg_resources.resource_filename("cg", RNAFUSION_BUNDLE_FILENAMES)
-)
+RNAFUSION_BUNDLE_FILENAMES_PATH = Path(project_root_dir, RNAFUSION_BUNDLE_FILENAMES)
 
-TAXPROFILER_BUNDLE_FILENAMES_PATH: Path = Path(
-    pkg_resources.resource_filename("cg", TAXPROFILER_BUNDLE_FILENAMES)
-)
+TAXPROFILER_BUNDLE_FILENAMES_PATH = Path(project_root_dir, TAXPROFILER_BUNDLE_FILENAMES)
 
-TOMTE_BUNDLE_FILENAMES_PATH: Path = Path(
-    pkg_resources.resource_filename("cg", TOMTE_BUNDLE_FILENAMES)
-)
+TOMTE_BUNDLE_FILENAMES_PATH = Path(project_root_dir, TOMTE_BUNDLE_FILENAMES)

cg/server/invoices/views.py

@@ -197,7 +197,7 @@ def invoice_template(invoice_id):
     workbook = render_xlsx(invoice_dict)
 
     temp_dir = tempfile.gettempdir()
-    filename = "Invoice_{}_{}.xlsx".format(invoice_obj.id, cost_center)
+    filename = f"Invoice_{invoice_obj.id}_{cost_center}.xlsx"
     excel_path = os.path.join(temp_dir, filename)
     workbook.save(excel_path)
 

cg/utils/files.py

@@ -1,25 +1,29 @@
-"""Some helper functions for working with files"""
+"""Some helper functions for working with files."""
 
 import logging
 import os
 import shutil
+from importlib.resources import files
 from pathlib import Path
 
 LOG = logging.getLogger(__name__)
 
 
+def get_project_root_dir() -> Path:
+    return Path(files("cg"))
+
+
 def get_file_in_directory(directory: Path, file_name: str) -> Path:
     """Get a file in a directory and subdirectories.
     Raises:
         FileNotFoundError: If the directory does not exist.
     """
     if not directory.is_dir() or not directory.exists():
         raise FileNotFoundError(f"Directory {directory} does not exist")
-    for directory_path, _, files in os.walk(directory):
-        for file in files:
+    for directory_path, _, dir_files in os.walk(directory):
+        for file in dir_files:
             if file_name == file:
-                path_to_file = Path(directory_path, file)
-                return path_to_file
+                return Path(directory_path, file)
     raise FileNotFoundError(f"File {file_name} not found in {directory}")
 
 
@@ -43,10 +47,10 @@ def get_files_in_directory_with_pattern(directory: Path, pattern: str) -> list[P
     files_with_pattern: list[Path] = []
     if not directory.is_dir() or not directory.exists():
         raise FileNotFoundError(f"Directory {directory} does not exist")
-    for directory_path, _, files in os.walk(directory):
-        for file in files:
-            if pattern in file:
-                files_with_pattern.append(Path(directory_path, file))
+    for directory_path, _, dir_files in os.walk(directory):
+        files_with_pattern.extend(
+            Path(directory_path, file) for file in dir_files if pattern in file
+        )
     if not files_with_pattern:
         raise FileNotFoundError(f"No files with pattern {pattern} found in {directory}")
     return files_with_pattern
@@ -117,9 +121,9 @@ def link_or_overwrite_file(src: Path, dst: Path) -> None:
 def get_all_files_in_directory_tree(directory: Path) -> list[Path]:
     """Get the relative paths of all files in a directory and its subdirectories."""
     files_in_directory: list[Path] = []
-    for subdir, _, files in os.walk(directory):
+    for subdir, _, dir_files in os.walk(directory):
         subdir = Path(subdir).relative_to(directory)
-        files_in_directory.extend([Path(subdir, file) for file in files])
+        files_in_directory.extend([Path(subdir, file) for file in dir_files])
     return files_in_directory
 
 

tests/utils/test_files.py

@@ -9,12 +9,21 @@
     get_file_with_pattern_from_list,
     get_files_in_directory_with_pattern,
     get_files_matching_pattern,
+    get_project_root_dir,
     get_source_creation_time_stamp,
     remove_directory_and_contents,
     rename_file,
 )
 
 
+def test_get_project_root_dir():
+    # WHEN getting the project root dir
+    root_dir: Path = get_project_root_dir()
+
+    # THEN return the dir path
+    assert root_dir.name == "cg"
+
+
 def test_get_file_in_directory(nested_directory_with_file: Path, some_file: str):
     """Test function to get a file in a directory and subdirectories."""
     # GIVEN a directory with subdirectories with a file