Add validator for filename

elixir-europe · Nov 5, 2024 · 859814e · 859814e
1 parent eb8881b
commit 859814e
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Showing 6 changed files with 73 additions and 15 deletions.
diff --git a/mars-cli/mars_lib/models/isa_json.py b/mars-cli/mars_lib/models/isa_json.py
@@ -1,4 +1,7 @@
 from __future__ import annotations
+
+import re
+
 from enum import Enum
 from typing import List, Optional, Union
 from pydantic import BaseModel, Field, field_validator, ConfigDict
@@ -189,6 +192,15 @@ class Assay(CommentedIsaBase):
     technologyType: Optional[OntologyAnnotation] = None
     unitCategories: List[OntologyAnnotation] = []
 
+    @field_validator("filename")
+    def validate_filename(cls, v: str) -> Union[str, None]:
+        if v is None:
+            return v
+        elif re.match(r"^a_", v):
+            return v
+        else:
+            raise ValueError("'filename' should start with 'a_'")
+
     @field_validator("comments")
     def detect_target_repo_comments(cls, v: List[Comment]) -> Optional[List[Comment]]:
         target_repo_comments = [
@@ -242,14 +254,14 @@ class MaterialAttribute(IsaBase):
 
 
 class Study(CommentedIsaBase):
-    id: Optional[str] = Field(alias="@id", default=None)
+    id: str = Field(alias="@id", default=None)
     assays: List[Assay] = []
     characteristicCategories: List[MaterialAttribute] = []
     description: Optional[str] = None
     factors: List[Factor] = []
     filename: Optional[str] = None
     identifier: Optional[str] = None
-    materials: Optional[StudyMaterialType]
+    materials: Optional[StudyMaterialType] = None
     people: List[Person] = []
     processSequence: List[Process] = []
     protocols: List[Protocol] = []
@@ -260,9 +272,18 @@ class Study(CommentedIsaBase):
     title: Optional[str] = None
     unitCategories: List[OntologyAnnotation] = []
 
+    @field_validator("filename")
+    def validate_filename(cls, v: str) -> Union[str, None]:
+        if v is None:
+            return v
+        elif re.match(r"^s_", v):
+            return v
+        else:
+            raise ValueError("'filename' should start with 's_'")
+
 
 class Investigation(CommentedIsaBase):
-    id: Optional[str] = Field(alias="@id", default=None)
+    id: str = Field(alias="@id", default=None)
     description: Optional[str] = None
     filename: Optional[str] = None
     identifier: Optional[str] = None
@@ -274,6 +295,15 @@ class Investigation(CommentedIsaBase):
     submissionDate: Optional[str] = None
     title: Optional[str] = None
 
+    @field_validator("filename")
+    def validate_filename(cls, v: str) -> Union[str, None]:
+        if v is None:
+            return v
+        elif re.match(r"^i_", v):
+            return v
+        else:
+            raise ValueError("'filename' should start with 'i_'")
+
 
 class IsaJson(IsaBase):
     investigation: Investigation
diff --git a/mars-cli/tests/test_isa_json.py b/mars-cli/tests/test_isa_json.py
@@ -1,3 +1,5 @@
+import re
+
 from mars_lib.isa_json import (
     reduce_isa_json_for_target_repo,
     load_isa_json,
@@ -6,7 +8,15 @@
 from mars_lib.target_repo import TargetRepository, TARGET_REPO_KEY
 import pytest
 from pydantic import ValidationError
-from mars_lib.models.isa_json import Data, Material, Assay, Person, IsaJson
+from mars_lib.models.isa_json import (
+    Data,
+    Material,
+    Assay,
+    Person,
+    IsaJson,
+    Investigation,
+    Study,
+)
 from mars_lib.models.repository_response import RepositoryResponse
 import json
 
@@ -225,3 +235,21 @@ def test_update_study_materials_with_accession_categories():
         updated_investigation.studies[0].materials.samples[0].characteristics[-1].value
         == repo_response.accessions[1].value
     )
+
+
+def test_filename_validation():
+    # ISA should have a filename that starts with 'x_'
+    with pytest.raises(ValidationError, match=f"'filename' should start with 'i_'"):
+        Investigation.model_validate({"@id": "1", "filename": "bad filename"})
+
+    with pytest.raises(ValidationError, match=f"'filename' should start with 's_'"):
+        Study.model_validate({"@id": "2", "filename": "bad filename"})
+
+    with pytest.raises(ValidationError, match=f"'filename' should start with 'a_'"):
+        Assay.model_validate({"@id": "3", "filename": "bad filename"})
+
+    assert re.match(r"^i_", "i_Good_file_name")
+
+    assert Investigation.model_validate({"@id": "4", "filename": "i_Good_File_Name"})
+    assert Study.model_validate({"@id": "5", "filename": "s_Good_File_Name"})
+    assert Assay.model_validate({"@id": "6", "filename": "a_Good_File_Name"})
diff --git a/test-data/biosamples-input-isa.json b/test-data/biosamples-input-isa.json
@@ -6,7 +6,7 @@
     "submissionDate": "",
     "publicReleaseDate": "",
     "ontologySourceReferences": [],
-    "filename": "Bob's investigation.txt",
+    "filename": "i_Bob's investigation.txt",
     "comments": [
       {
         "name": "ISAjson export time",
@@ -60,7 +60,7 @@
         "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
         "submissionDate": "",
         "publicReleaseDate": "",
-        "filename": "Arabidopsis thaliana.txt",
+        "filename": "s_Arabidopsis thaliana.txt",
         "comments": [
           {
             "name": "SEEK Study ID",
@@ -1008,4 +1008,4 @@
       }
     ]
   }
-}
+}
diff --git a/test-data/biosamples-modified-isa.json b/test-data/biosamples-modified-isa.json
@@ -6,7 +6,7 @@
     "submissionDate": "",
     "publicReleaseDate": "",
     "ontologySourceReferences": [],
-    "filename": "Bob's investigation.txt",
+    "filename": "i_Bob's investigation.txt",
     "comments": [
       {
         "name": "ISAjson export time",
@@ -60,7 +60,7 @@
         "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
         "submissionDate": "",
         "publicReleaseDate": "",
-        "filename": "Arabidopsis thaliana.txt",
+        "filename": "s_Arabidopsis thaliana.txt",
         "comments": [
           {
             "name": "SEEK Study ID",
@@ -1019,4 +1019,4 @@
       }
     ]
   }
-}
+}
diff --git a/test-data/biosamples-original-isa-no-accesion-char.json b/test-data/biosamples-original-isa-no-accesion-char.json
@@ -6,7 +6,7 @@
       "submissionDate": "",
       "publicReleaseDate": "",
       "ontologySourceReferences": [],
-      "filename": "Bob's investigation.txt",
+      "filename": "i_Bob's investigation.txt",
       "comments": [
          {
             "name": "ISAjson export time",
@@ -60,7 +60,7 @@
             "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
             "submissionDate": "",
             "publicReleaseDate": "",
-            "filename": "Arabidopsis thaliana.txt",
+            "filename": "s_Arabidopsis thaliana.txt",
             "comments": [
                {
                   "name": "SEEK Study ID",

diff --git a/test-data/biosamples-original-isa.json b/test-data/biosamples-original-isa.json
@@ -6,7 +6,7 @@
       "submissionDate": "",
       "publicReleaseDate": "",
       "ontologySourceReferences": [],
-      "filename": "Bob's investigation.txt",
+      "filename": "i_Bob's investigation.txt",
       "comments": [
          {
             "name": "ISAjson export time",
@@ -60,7 +60,7 @@
             "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
             "submissionDate": "",
             "publicReleaseDate": "",
-            "filename": "Arabidopsis thaliana.txt",
+            "filename": "s_Arabidopsis thaliana.txt",
             "comments": [
                {
                   "name": "SEEK Study ID",
@@ -1002,4 +1002,4 @@
          }
       ]
    }
-}
+}