Dynamic errors

src/cap_upload_validator/errors.py

@@ -1,25 +1,25 @@
-from typing import List
+from typing import List, Optional
 
 
 class CapException(BaseException):
     name = "Unknown"
-    message = "Useless CAP exception"
+    message = "Generic CAP exception"
 
     def __str__(self) -> str:
         return f"{self.name}: {self.message}"
 
     def __eq__(self, other):
         if isinstance(other, CapException):
             return (self.name, self.message) == (other.name, other.message)
-        raise TypeError(f"The __eq__ operation doesn't defined for CapException and {type(other)}!")
+        raise TypeError(f"The __eq__ operation is not defined for CapException and {type(other)}!")
 
     def __hash__(self):
         return hash((self.name, self.message))
 
 
 class BadAnnDataFile(CapException):
-    name = 'Unknown'
-    message = 'File format is not supported!'
+    name = 'BadAnnDataFile'
+    message = 'The file format is not supported!'
 
 
 class CapMultiException(CapException):
@@ -57,8 +57,11 @@ def append(self, other: CapException) -> None:
     def __str__(self) -> str:
         own_str = super().__str__()
         res_list = [own_str] + self.ex_list
-        res_message = "\n".join(map(str, res_list))
-        res_message += "\nFor details visit: \n\thttps://github.com/cellannotation/cap-validator/wiki/Validation-Errors"
+        res_message = "\n\n".join(map(str, res_list))
+        res_message += (
+            "\n\nFor details visit:\n"
+            "\thttps://github.com/cellannotation/cap-validator/wiki/Validation-Errors"
+        )
         return res_message
 
     def have_errors(self) -> bool:
@@ -71,48 +74,107 @@ def to_list(self) -> List[CapException]:
         return self.ex_list
 
 
-class AnnDataFileMissingCountMatrix(CapException):
-    name = "AnnDataFileMissingCountMatrix"
-    message = "DataFile Incorrect format: raw data matrix is missing in .raw.X or .X."
+class AnnDataMissingCountMatrix(CapException):
+    name = "AnnDataMissingCountMatrix"
+    message = "Matrix is missing in both `.X` and `.raw.X`."
+
+
+class AnnDataInvalidCountMatrix(CapException):
+    name = "AnnDataInvalidCountMatrix"
+    message = "Raw counts matrix values must be non-negative integers."
 
 
 class AnnDataMissingEmbeddings(CapException):
     name = "AnnDataMissingEmbeddings"
-    message = \
-        """
-        The embedding is missing or is incorrectly named: embeddings must be a [n_cells x 2] 
-        numpy array saved with the prefix X_, for example: X_tsne, X_pca or X_umap.
-        """
+    message = (
+        "Embeddings are missing or incorrectly formatted. "
+        "They must be stored in `.obsm` as [n_cells × 2] datasets "
+        "with names starting with 'X_' (e.g., X_umap, X_tsne)."
+    )
+
+
+class AnnDataMissingObs(CapException):
+    name = "AnnDataMissingObs"
+    message = "The `.obs` is missing."
 
 
 class AnnDataMissingObsColumns(CapException):
     name = "AnnDataMissingObsColumns"
-    message = \
-        """
-            Required obs column(s) missing: file must contain 
-            'assay', 'disease', 'organism' and 'tissue' fields or
-            corresponding '<x>_ontology_term_id' fields with valid values.
-        """
 
-class AnnDataNoneInGeneralMetadata(CapException):
-    name = "AnnDataNoneInGeneralMetadata"
-    message = \
-        """
-            Required obs column(s) contain empty or None values: file must contain 
-            'assay', 'disease', 'organism' and 'tissue' fields or
-            corresponding '<x>_ontology_term_id' fields with valid values.
-        """
+    def __init__(self, missing_columns: list[str] = None):
+        msg = (
+            "Required `.obs` metadata is missing. The file must contain "
+            "'assay', 'disease', 'organism', 'tissue' "
+            "or corresponding '<x>_ontology_term_id' fields."
+        )
+        if missing_columns:
+            cols_str = ", ".join(missing_columns)
+            self.message = f"{msg}\nMissing columns: {cols_str}"
+        else:
+            self.message = msg
+
+
+class AnnDataEmptyOrNoneInGeneralMetadata(CapException):
+    name = "AnnDataEmptyOrNoneInGeneralMetadata"
+
+    def __init__(
+        self,
+        none_columns: Optional[List[str]] = None,
+        empty_columns: Optional[List[str]] = None,
+    ):
+        msg = (
+            "Required `.obs` metadata contains missing or invalid values.\n"
+            "All required fields must be filled with valid values."
+        )
+
+        if none_columns:
+            msg += "\nColumns with None / NaN values: " + ", ".join(sorted(none_columns))
+
+        if empty_columns:
+            msg += "\nColumns with empty values: " + ", ".join(sorted(empty_columns))
+
+        self.message = msg
+
 
 class AnnDataNonStandardVarError(CapException):
     name = "AnnDataNonStandardVarError"
-    message = \
-        """
-            File does not contain valid ENSEMBL terms in var.
-            We currently support Homo sapiens and Mus musculus.
-            In the case of multiple species in the dataset, orthologous Homo sapiens genes are required.
-            If there are other species you wish to upload to CAP, please contact
-            support@celltype.info and we will work to accommodate your request.
-        """ 
+
+
+class AnnDataMissingVarIndex(AnnDataNonStandardVarError):
+    name = "AnnDataMissingVarIndex"
+    message = "The `.var.index` is missing or empty."
+
+
+class AnnDataNumericVarIndex(AnnDataNonStandardVarError):
+    name = "AnnDataNumericVarIndex"
+    message = "The `.var.index` contains numeric values instead of gene identifiers."
+
+
+class AnnDataVarNotSubsetOfRawVar(AnnDataNonStandardVarError):
+    name = "AnnDataVarNotSubsetOfRawVar"
+    message = "`var.index` must be a subset of `raw.var.index`."
+
+
+class AnnDataGeneIndexIsNotUnique(AnnDataNonStandardVarError):
+    name = "AnnDataGeneIndexIsNotUnique"
+    message = "`var.index` must not contain duplicates."
+
+
+class AnnDataUnsupportedGenes(AnnDataNonStandardVarError):
+    name = "AnnDataUnsupportedGenes"
+
+    def __init__(self, missing_genes_count: int = None):
+        msg = (
+            "File does not contain valid ENSEMBL terms in var.\n"
+            "We currently support only Homo sapiens and Mus musculus.\n"
+            "In the case of multiple species in the dataset, orthologous Homo sapiens genes are required.\n"
+            "If there are other species you wish to upload to CAP, please contact "
+            "support@celltype.info and we will work to accommodate your request."
+        )
+        if missing_genes_count is not None:
+            msg += f"\nNumber of unsupported genes found: {missing_genes_count}"
+        self.message = msg
+
 
 class CSCMatrixInX(CapException):
     name = "CSCMatrixInX"
@@ -125,6 +187,6 @@ def __init__(self, locations: list[str]):
         self.locations = locations
         loc_str = " and ".join(locations)
         self.message = (
-            f"The CSC matrix is found in {loc_str}. "
-            "Gene expression matrix must be stored in CSR or dense format!"
+            f"A CSC matrix is found in {loc_str}. "
+            "The gene expression matrix must be stored in CSR or dense format!"
         )