Store demo case file paths as absolute paths

CHANGELOG.md

@@ -11,6 +11,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - All links in disease table on diagnosis page now open in a new tab
 - Dark mode settings applied to multiselects on institute settings
 - Comments on case and variant pages can be viewed by expanding an accordion
+- Demo case file paths are now stored as absolute paths
 ### Fixed
 - On variants page, search for variants in genes present only in build 38 returning no results
 - Pin/unpin with API was not able to make event links

scout/models/case/case_loading_models.py

@@ -4,6 +4,7 @@
 from enum import Enum
 from fractions import Fraction
 from glob import glob
+from os.path import abspath, exists, isabs
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
@@ -12,7 +13,6 @@
 except ImportError:
     from typing_extensions import Literal
 
-import path
 from pydantic import BaseModel, Field, field_validator, model_validator
 
 from scout.constants import ANALYSIS_TYPES
@@ -49,7 +49,11 @@
     "peddy_ped",
     "peddy_ped_check",
     "peddy_sex_check",
+    "exe_ver",
+    "smn_tsv",
+    "reference_info",
     "RNAfusion_inspector",
+    "RNAfusion_inspector_research",
     "RNAfusion_report",
     "RNAfusion_report_research",
 ]
@@ -86,18 +90,14 @@ class Sex(str, Enum):
     unknown = "unknown"
 
 
-def _get_demo_file_absolute_path(partial_path: str) -> str:
-    """returns the absolute path to a given demo file."""
-    APP_ROOT: str = path.abspath(path.join(path.dirname(__file__), ".."))
-    return path.join(APP_ROOT, partial_path)
-
-
-def _is_string_path(string_path: str) -> bool:
-    try:
-        path = Path(string_path) or Path(_get_demo_file_absolute_path(partial_path=string_path))
-        return path.is_file()
-    except AttributeError:
-        return False
+def _resource_abs_path(string_path: str) -> str:
+    """Return the absolute path to a resource file."""
+    if exists(string_path) and isabs(string_path):
+        return string_path
+    elif exists(string_path):
+        return abspath(string_path)
+    else:
+        raise FileExistsError(f"File {string_path} could not be found on disk.")
 
 
 #### VCF files class ####
@@ -125,9 +125,8 @@ def validate_file_path(cls, values: Dict) -> "VcfFiles":
         """Make sure that VCF file exists on disk."""
         for item in VCF_FILE_PATH_CHECKS:
             item_path: str = values.get(item)
-            if item_path and _is_string_path(values[item]) is False:
-                raise ValueError(f"{item} path '{values[item]}' is not valid.")
-
+            if item_path:
+                values[item] = _resource_abs_path(item_path)
         return values
 
 
@@ -246,8 +245,8 @@ def validate_file_path(cls, values: Dict) -> "SampleLoader":
         """Make sure that files associated to samples (mostly alignment files) exist on disk."""
         for item in SAMPLES_FILE_PATH_CHECKS:
             item_path: str = values.get(item)
-            if item_path and _is_string_path(values[item]) is False:
-                raise ValueError(f"{item} path '{values[item]}' is not valid.")
+            if item_path:
+                values[item] = _resource_abs_path(item_path)
 
         return values
 
@@ -283,7 +282,7 @@ def check_image_path(cls, path: str) -> Optional[str]:
             raise TypeError(
                 f"Custom images should be of type: {', '.join(SUPPORTED_IMAGE_FORMATS)}"
             )
-        if REPID not in path and _is_string_path(path) is False:
+        if REPID not in path and exists(path) is False:
             raise ValueError(f"Image path '{path}' is not valid.")
         return path
 
@@ -387,6 +386,7 @@ class CaseLoader(BaseModel):
     peddy_sex_check: Optional[str] = Field(None, alias="peddy_sex")  # Soon to be deprecated
     phenotype_groups: Optional[List[str]] = None
     phenotype_terms: Optional[List[str]] = None
+    exe_ver: Optional[str] = None
     rank_model_version: Optional[str] = None
     rank_score_threshold: Optional[int] = 0
     reference_info: Optional[str] = None
@@ -502,8 +502,8 @@ def validate_file_path(cls, values: Dict) -> "CaseLoader":
         """Make sure the files associated to the case (mostly reports) exist on disk."""
         for item in CASE_FILE_PATH_CHECKS:
             item_path: str = values.get(item)
-            if item_path and _is_string_path(values[item]) is False:
-                raise ValueError(f"{item} path '{values[item]}' is not valid.")
+            if item_path:
+                values[item] = _resource_abs_path(item_path)
 
         return values
 

tests/parse/test_parse_case.py

@@ -1,5 +1,6 @@
 import logging
 from datetime import datetime
+from os import path
 
 import pytest
 from pydantic import ValidationError
@@ -73,8 +74,8 @@ def test_parse_case_parsing(scout_config, param_name):
     # GIVEN you load sample information from a scout config
     # WHEN case is parsed
     case_data = parse_case_config(scout_config)
-    # THEN the case should have the parameter
-    assert case_data[param_name] == scout_config[param_name]
+    # THEN the case should have the parameter, either as string of full path to a resource
+    assert case_data[param_name] == scout_config[param_name] or path.exists(case_data[param_name])
 
 
 @pytest.mark.parametrize(
@@ -193,8 +194,9 @@ def test_parse_case_vcf_files(scout_config, vcf_file):
     # GIVEN you load sample information from a scout config
     # WHEN case is parsed
     case_data = parse_case_config(scout_config)
-    # THEN the case should the same vcf files as specified in the
-    assert case_data["vcf_files"][vcf_file] == scout_config[vcf_file]
+
+    # THEN the case should contain the absolute path to the resources specified in the case config
+    assert path.exists(case_data["vcf_files"][vcf_file])
 
 
 @pytest.mark.parametrize("bam_name", ["alignment_path", "bam_file", "bam_path"])