merging in pyright-ratchet-errors.txt additions

Author: pgm

portal-backend/pyright-ratchet-errors.txt

@@ -6,6 +6,7 @@ api.py: error: Argument of type "Column[int]" cannot be assigned to parameter "n
 api.py: error: Argument of type "Column[str]" cannot be assigned to parameter "name" of type "str" in function "__init__"
 api.py: error: Argument of type "Column[str]" cannot be assigned to parameter "subtype_code" of type "str" in function "get_model_ids_by_subtype_code_and_node_level"
 api.py: error: Argument of type "dict[bool, str]" cannot be assigned to parameter "func" of type "PythonFuncType" in function "map" (reportArgumentType)
+api.py: error: Argument of type "dict[str, str]" cannot be assigned to parameter "func" of type "PythonFuncType" in function "map"
 api.py: error: Argument of type "float | None" cannot be assigned to parameter "max_fdr" of type "float" in function "get_sig_context_dataframe"
 api.py: error: Argument of type "float | None" cannot be assigned to parameter "min_abs_effect_size" of type "float" in function "get_sig_context_dataframe"
 api.py: error: Argument of type "float | None" cannot be assigned to parameter "min_frac_dep_in" of type "float" in function "get_sig_context_dataframe"
@@ -296,13 +297,22 @@ index.py: error: Argument of type "Column[int]" cannot be assigned to parameter
 index.py: error: Argument of type "Column[int]" cannot be assigned to parameter "entity_id" of type "int" in function "get_relation_to_entity"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "compound_id" of type "str" in function "get_all_datasets_containing_compound"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "compound_id" of type "str" in function "get_heatmap_dose_curves_tab_drc_options"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "compound_id" of type "str" in function "get_predictive_models_for_compound"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "compound_label" of type "str" in function "get_heatmap_dose_curves_tab_drc_options"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "dataset_given_id" of type "str" in function "get_correlation_for_entity"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "dataset_id" of type "str" in function "get_dataset_label"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "key" of type "str" in function "__getitem__"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "key" of type "str" in function "get"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_dataset_given_id" of type "str" in function "get_interactive_url_for_entity"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_feature_id" of type "str" in function "get_correlation_for_entity"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_feature_id" of type "str" in function "get_interactive_url_for_entity"
+index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_feature_id" of type "str" in function "get_relation_to_entity"
 index.py: error: Argument of type "Column[str]" cannot be assigned to parameter "row_name" of type "str" in function "valid_row"
 index.py: error: Argument of type "DependencyDataset | None" cannot be assigned to parameter "object" of type "DependencyDataset" in function "append"
+index.py: error: Argument of type "str | None" cannot be assigned to parameter "pred_model_feature_type" of type "str" in function "get_relation_to_entity"
 index.py: error: Argument of type "str | None" cannot be assigned to parameter "x" of type "ConvertibleToInt" in function "__new__"
 index.py: error: Cannot access attribute "any" for class "List[Gene]"
+index.py: error: Cannot access attribute "entrez_id" for class "Entity"
 index.py: error: Cannot access attribute "has" for class "DependencyDataset"
 index.py: error: Cannot access attribute "has" for class "Entity"
 index.py: error: Invalid conditional operand of type "Column[int]"
@@ -365,16 +375,22 @@ models.py: error: "matrix" is not a known attribute of "None" (reportOptionalMem
 models.py: error: "RelationshipProperty[Any]" is not iterable
 models.py: error: "taiga_id" is not a known attribute of "None" (reportOptionalMemberAccess)
 models.py: error: Argument of type "ArrayLike | float | Number | number[Any, int | float | complex] | Index | Series | Unknown | ArrowExtensionArray | NAType | NaTType | Timestamp | Timedelta | Any | DatetimeIndex | TimedeltaIndex | BooleanArray | FloatingArray | IntegerArray | ndarray[_AnyShape, dtype[signedinteger[_64Bit]]]" cannot be assigned to parameter "x" of type "ConvertibleToFloat" in function "__new__"
+models.py: error: Argument of type "Column[int]" cannot be assigned to parameter "entity_id" of type "int" in function "get"
 models.py: error: Argument of type "Column[int]" cannot be assigned to parameter "entity_id" of type "int" in function "integrate_size_and_label_data"
 models.py: error: Argument of type "Column[int]" cannot be assigned to parameter "entity_id" of type "int" in function "legacy_dataset_contains_entity"
 models.py: error: Argument of type "Column[str] | str" cannot be assigned to parameter "s" of type "str | bytes | bytearray" in function "loads"
+models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "dataset_given_id" of type "str" in function "get_correlation_for_entity"
+models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "dataset_id" of type "str" in function "get_dataset_feature_type"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "dataset_id" of type "str" in function "get_dataset_label"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "feature_label" of type "str" in function "get_entity_summary_metadata"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "feature_label" of type "str" in function "get_feature_data"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "feature" of type "str" in function "get_row_of_values"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "file_path" of type "str" in function "get_row_of_values"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "key" of type "str" in function "get"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "paths" of type "BytesPath" in function "join"
+models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_dataset_given_id" of type "str" in function "get_interactive_url_for_entity"
+models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_feature_id" of type "str" in function "get_correlation_for_entity"
+models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "pred_model_feature_id" of type "str" in function "get_interactive_url_for_entity"
 models.py: error: Argument of type "Column[str]" cannot be assigned to parameter "s" of type "str | bytes | bytearray" in function "loads"
 models.py: error: Argument of type "Column[TabularEnum]" cannot be assigned to parameter "key" of type "BiomarkerEnum | DependencyEnum | TabularEnum" in function "__getitem__"
 models.py: error: Argument of type "Column[TabularEnum]" cannot be assigned to parameter "key" of type "TabularEnum" in function "__getitem__"
@@ -383,6 +399,7 @@ models.py: error: Argument of type "List[str] | None" cannot be assigned to para
 models.py: error: Argument of type "list[str]" cannot be assigned to parameter "columns" of type "Axes | None" in function "__init__"
 models.py: error: Argument of type "RelationshipProperty[Any]" cannot be assigned to parameter "onclause" of type "_OnClauseArgument | None" in function "join"
 models.py: error: Argument of type "RelationshipProperty[Any]" cannot be assigned to parameter "onclause" of type "_OnClauseArgument | None" in function "outerjoin"
+models.py: error: Argument of type "str | None" cannot be assigned to parameter "pred_model_feature_type" of type "str" in function "get_relation_to_entity"
 models.py: error: Argument of type "Unknown | Column[int]" cannot be assigned to parameter "index" of type "int" in function "get_row_of_values"
 models.py: error: Cannot access attribute "__table__" for class "type[Fusion]"
 models.py: error: Cannot access attribute "__table__" for class "type[Mutation]"
@@ -396,6 +413,7 @@ models.py: error: Cannot access attribute "download_file" for class "_File*"
 models.py: error: Cannot access attribute "gene" for class "_Gene*"
 models.py: error: Cannot access attribute "name" for class "Dataset*"
 models.py: error: Cannot access attribute "nominal_range" for class "TabularDatasetMeta"
+models.py: error: Cannot access attribute "target_gene" for class "Gene"
 models.py: error: Cannot access attribute "unique" for class "ndarray[_AnyShape, dtype[Any]]"
 models.py: error: Cannot assign to attribute "funding" for class "DownloadRelease*"
 models.py: error: Expression of type "None" cannot be assigned to parameter of type "Dict[int, GroupAuthConfig]"
@@ -477,6 +495,7 @@ predictability_loader.py: error: Invalid conditional operand of type "ColumnElem
 predictability_loader.py: error: No overloads for "get" match the provided arguments (reportCallIssue)
 predictability_loader.py: error: No overloads for "read_csv" match the provided arguments (reportCallIssue)
 predictability_loader.py: error: No parameter named "background" (reportCallIssue)
+predictability_loader.py: error: No parameter named "dataset_given_id" (reportCallIssue)
 predictability_loader.py: error: No parameter named "dataset_id" (reportCallIssue)
 predictability_loader.py: error: No parameter named "dataset" (reportCallIssue)
 predictability_loader.py: error: No parameter named "feature_id" (reportCallIssue)
@@ -706,9 +725,13 @@ transcription_start_site_loader.py: error: No parameter named "gene_id" (reportC
 transcription_start_site_loader.py: error: No parameter named "label" (reportCallIssue)
 transcription_start_site_loader.py: error: No parameter named "three_prime_position" (reportCallIssue)
 util.py: error: Expression of type "None" cannot be assigned to parameter of type "Client"
+util.py: error: Expression of type "None" cannot be assigned to return type "str"
 util.py: error: Type "None" is not assignable to return type "str"
+utils.py: error: "abs_dest_path" is possibly unbound (reportPossiblyUnboundVariable)
+utils.py: error: "base_name" is possibly unbound (reportPossiblyUnboundVariable)
 utils.py: error: Argument of type "list[Column[str]]" cannot be assigned to parameter "path" of type "List[str]" in function "__init__"
 utils.py: error: Argument of type "Unknown | None" cannot be assigned to parameter "string" of type "bytes | bytearray" in function "quote"
+utils.py: error: Argument of type "Unknown | None" cannot be assigned to parameter "string" of type "bytes | bytearray" in function "quote" (reportArgumentType)
 utils.py: error: Cannot assign to attribute "_depmap_interactive_config" for class "Flask"
 utils.py: error: Cannot assign to attribute "_depmap_taiga_id_to_download_url" for class "Flask"
 utils.py: error: Invalid conditional operand of type "ColumnElement[bool]"
@@ -769,6 +792,7 @@ views.py: error: Argument of type "Unknown | None" cannot be assigned to paramet
 views.py: error: Argument to class must be a base class (reportGeneralTypeIssues)
 views.py: error: Cannot access attribute "any" for class "List[Gene]"
 views.py: error: Cannot access attribute "apply" for class "FunctionType"
+views.py: error: Cannot access attribute "compound_id" for class "Entity"
 views.py: error: Cannot access attribute "entrez_id" for class "Entity"
 views.py: error: Cannot access attribute "rename" for class "float"
 views.py: error: Cannot access attribute "rename" for class "int"