Improve error messages.

tanaylab · Jun 8, 2024 · fb0dbe9 · fb0dbe9
1 parent a73a224
commit fb0dbe9
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diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-06-07T09:50:19","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-06-08T11:10:42","documenter_version":"1.4.1"}}
diff --git a/src/concat.jl b/src/concat.jl
@@ -166,7 +166,7 @@ By default, concatenation will fail rather than `overwrite` existing properties
         for axis in axes
             require_no_axis(destination, axis)
             for source in sources
-                require_axis(source, axis)
+                require_axis(source, "for: concatenate!", axis)
             end
         end
 

diff --git a/src/queries.jl b/src/queries.jl
@@ -1871,7 +1871,7 @@ function fake_query_operation!(fake_query_state::FakeQueryState, axis::Axis)::No
 end
 
 function push_axis(query_state::QueryState, axis::Axis, ::Nothing)::Nothing
-    require_axis(query_state.daf, axis.axis_name)
+    require_axis(query_state.daf, "for the query: $(query_state.query_sequence)", axis.axis_name)
     query_sequence = QuerySequence((axis,))
     dependency_keys = Set((Formats.axis_array_cache_key(axis.axis_name),))
     axis_state = AxisState(query_sequence, dependency_keys, axis.axis_name, nothing)

diff --git a/src/readers.jl b/src/readers.jl
@@ -217,7 +217,7 @@ function axis_array(
             else
                 result_prefix = "default "
                 @assert default == undef
-                require_axis(daf, axis)
+                require_axis(daf, "for: axis_array", axis)
             end
         end
 
@@ -234,7 +234,7 @@ Return a dictionary converting axis entry names to their integer index.
 """
 function axis_dict(daf::DafReader, axis::AbstractString)::AbstractDict{<:AbstractString, <:Integer}
     return Formats.with_data_read_lock(daf, "axis_dict of:", axis) do
-        require_axis(daf, axis)
+        require_axis(daf, "for: axis_dict", axis)
         result = Formats.axis_dict_with_cache(daf, axis)
         @debug "axis_dict daf: $(depict(daf)) result: $(depict(result))"
         return result
@@ -250,16 +250,16 @@ This first verifies the `axis` exists in `daf`.
 """
 function axis_length(daf::DafReader, axis::AbstractString)::Int64
     return Formats.with_data_read_lock(daf, "axis_length of:", axis) do
-        require_axis(daf, axis)
+        require_axis(daf, "for: axis_length", axis)
         result = Formats.format_axis_length(daf, axis)
         @debug "axis_length daf: $(depict(daf)) axis: $(axis) result: $(result)"
         return result
     end
 end
 
-function require_axis(daf::DafReader, axis::AbstractString; for_change::Bool = false)::Nothing
+function require_axis(daf::DafReader, what_for::AbstractString, axis::AbstractString; for_change::Bool = false)::Nothing
     if !Formats.format_has_axis(daf, axis; for_change = for_change)
-        error("missing axis: $(axis)\nin the daf data: $(daf.name)")
+        error("missing axis: $(axis)\n$(what_for)\nof the daf data: $(daf.name)")
     end
     return nothing
 end
@@ -274,7 +274,7 @@ This first verifies the `axis` exists in `daf`.
 """
 function has_vector(daf::DafReader, axis::AbstractString, name::AbstractString)::Bool
     return Formats.with_data_read_lock(daf, "has_vector of:", name, "of:", axis) do
-        require_axis(daf, axis)
+        require_axis(daf, "for has_vector: $(name)", axis)
         result = name == "name" || Formats.format_has_vector(daf, axis, name)
         @debug "has_vector daf: $(depict(daf)) axis: $(axis) name: $(name) result: $(result)"
         return result
@@ -313,7 +313,7 @@ This first verifies the `axis` exists in `daf`.
 """
 function vectors_set(daf::DafReader, axis::AbstractString)::AbstractSet{<:AbstractString}
     return Formats.with_data_read_lock(daf, "vectors_set of:", axis) do
-        require_axis(daf, axis)
+        require_axis(daf, "for: vectors_set", axis)
         result = Formats.get_vectors_set_through_cache(daf, axis)
         @debug "vectors_set daf: $(depict(daf)) axis: $(axis) result: $(depict(result))"
         return result
@@ -344,10 +344,10 @@ function get_vector(
     default::Union{StorageScalar, StorageVector, Nothing, UndefInitializer} = undef,
 )::Maybe{NamedArray}
     return Formats.with_data_read_lock(daf, "get_vector of:", name, "of:", axis) do
-        require_axis(daf, axis)
+        require_axis(daf, "for the vector: $(name)", axis)
 
         if default isa StorageVector
-            require_axis_length(daf, "default length", length(default), axis)
+            require_axis_length(daf, length(default), "default for the vector: $(name)", axis)
             if default isa NamedVector
                 require_dim_name(daf, axis, "default dim name", dimnames(default, 1))
                 require_axis_names(daf, axis, "entry names of the: default", names(default, 1))
@@ -449,8 +449,8 @@ function has_matrix(
     return Formats.with_data_read_lock(daf, "has_matrix of:", name, "of:", rows_axis, "and:", columns_axis) do
         Formats.relayout = relayout && rows_axis != columns_axis
 
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         result = with_read_lock(daf.internal.cache_lock) do
             return haskey(daf.internal.cache, Formats.matrix_cache_key(rows_axis, columns_axis, name)) ||
@@ -490,8 +490,8 @@ function matrices_set(
     return Formats.with_data_read_lock(daf, "matrices_set of:", rows_axis, "and:", columns_axis) do
         relayout = relayout && rows_axis != columns_axis
 
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of: matrices_set", rows_axis)
+        require_axis(daf, "for the columns of: matrices_set", columns_axis)
 
         if !relayout
             names = Formats.get_matrices_set_through_cache(daf, rows_axis, columns_axis)
@@ -594,13 +594,13 @@ function do_get_matrix(
 )::Maybe{NamedArray}
     relayout = relayout && rows_axis != columns_axis
 
-    require_axis(daf, rows_axis)
-    require_axis(daf, columns_axis)
+    require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+    require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
     if default isa StorageMatrix
         require_column_major(default)
-        require_axis_length(daf, "default rows", size(default, Rows), rows_axis)
-        require_axis_length(daf, "default columns", size(default, Columns), columns_axis)
+        require_axis_length(daf, size(default, Rows), "rows of the default for the matrix: $(name)", rows_axis)
+        require_axis_length(daf, size(default, Columns), "columns of the default for the matrix: $(name)", columns_axis)
         if default isa NamedMatrix
             require_dim_name(daf, rows_axis, "default rows dim name", dimnames(default, 1); prefix = "rows")
             require_dim_name(daf, columns_axis, "default columns dim name", dimnames(default, 2); prefix = "columns")
@@ -767,13 +767,14 @@ end
 
 function require_axis_length(
     daf::DafReader,
-    what_name::AbstractString,
     what_length::StorageInteger,
+    vector_name::AbstractString,
     axis::AbstractString,
 )::Nothing
     if what_length != Formats.format_axis_length(daf, axis)
         error(
-            "$(what_name): $(what_length)\n" *
+            "the length: $(what_length)\n" *
+            "of the $(vector_name)\n" *
             "is different from the length: $(Formats.format_axis_length(daf, axis))\n" *
             "of the axis: $(axis)\n" *
             "in the daf data: $(daf.name)",

diff --git a/src/writers.jl b/src/writers.jl
@@ -168,7 +168,7 @@ function delete_axis!(daf::DafWriter, axis::AbstractString; must_exist::Bool = t
         @debug "delete_axis! daf: $(depict(daf)) axis: $(axis) must exist: $(must_exist)"
 
         if must_exist
-            require_axis(daf, axis; for_change = true)
+            require_axis(daf, "for: delete_axis!", axis; for_change = true)
         elseif !Formats.format_has_axis(daf, axis; for_change = true)
             return nothing
         end
@@ -248,10 +248,10 @@ function set_vector!(
         @debug "set_vector! daf: $(depict(daf)) axis: $(axis) name: $(name) vector: $(depict(vector)) overwrite: $(overwrite)"
 
         require_not_name(daf, axis, name)
-        require_axis(daf, axis)
+        require_axis(daf, "for the vector: $(name)", axis)
 
         if vector isa StorageVector
-            require_axis_length(daf, "vector length", length(vector), axis)
+            require_axis_length(daf, length(vector), "vector: $(name)", axis)
             if vector isa NamedVector
                 require_dim_name(daf, axis, "vector dim name", dimnames(vector, 1))
                 require_axis_names(daf, axis, "entry names of the: vector", names(vector, 1))
@@ -323,7 +323,7 @@ function get_empty_dense_vector!(
     try
         @debug "empty_dense_vector! daf: $(depict(daf)) axis: $(axis) name: $(name) eltype: $(eltype) overwrite: $(overwrite) {"
         require_not_name(daf, axis, name)
-        require_axis(daf, axis)
+        require_axis(daf, "for the vector: $(name)", axis)
 
         Formats.invalidate_cached!(daf, Formats.vectors_set_cache_key(axis))
         Formats.invalidate_cached!(daf, Formats.vector_cache_key(axis, name))
@@ -428,7 +428,7 @@ function get_empty_sparse_vector!(
     try
         @debug "empty_sparse_vector! daf: $(depict(daf)) axis: $(axis) name: $(name) eltype: $(eltype) nnz: $(nnz) indtype: $(indtype) overwrite: $(overwrite) {"
         require_not_name(daf, axis, name)
-        require_axis(daf, axis)
+        require_axis(daf, "for the vector: $(name)", axis)
 
         Formats.invalidate_cached!(daf, Formats.vector_cache_key(axis, name))
         Formats.invalidate_cached!(daf, Formats.vectors_set_cache_key(axis))
@@ -498,7 +498,7 @@ function delete_vector!(
         @debug "delete_vector! $daf: $(depict(daf)) axis: $(axis) name: $(name) must exist: $(must_exist)"
 
         require_not_name(daf, axis, name)
-        require_axis(daf, axis)
+        require_axis(daf, "for the vector: $(name)", axis)
 
         if must_exist
             require_vector(daf, axis, name)
@@ -561,13 +561,13 @@ function set_matrix!(
         relayout = relayout && rows_axis != columns_axis
         @debug "set_matrix! daf: $(depict(daf)) rows_axis: $(rows_axis) columns_axis: $(columns_axis) name: $(name) matrix: $(depict(matrix)) overwrite: $(overwrite) relayout: $(relayout)"
 
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         if matrix isa StorageMatrix
             require_column_major(matrix)
-            require_axis_length(daf, "matrix rows", size(matrix, Rows), rows_axis)
-            require_axis_length(daf, "matrix columns", size(matrix, Columns), columns_axis)
+            require_axis_length(daf, size(matrix, Rows), "rows of the matrix: $(name)", rows_axis)
+            require_axis_length(daf, size(matrix, Columns), "columns of the matrix: $(name)", columns_axis)
             if matrix isa NamedMatrix
                 require_dim_name(daf, rows_axis, "matrix rows dim name", dimnames(matrix, 1); prefix = "rows")
                 require_dim_name(daf, columns_axis, "matrix columns dim name", dimnames(matrix, 2); prefix = "columns")
@@ -651,8 +651,8 @@ function get_empty_dense_matrix!(
     Formats.begin_data_write_lock(daf, "empty_dense_matrix! of:", name, "of:", rows_axis, "and:", columns_axis)
     try
         @debug "empty_dense_matrix! daf: $(depict(daf)) rows_axis: $(rows_axis) columns_axis: $(columns_axis) name: $(name) eltype: $(eltype) overwrite: $(overwrite) {"
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         if !overwrite
             require_no_matrix(daf, rows_axis, columns_axis, name; relayout = false)
@@ -762,8 +762,8 @@ function get_empty_sparse_matrix!(
     Formats.begin_data_write_lock(daf, "empty_sparse_matrix! of:", name, "of:", rows_axis, "and:", columns_axis)
     try
         @debug "empty_sparse_matrix! daf: $(depict(daf)) rows_axis: $(rows_axis) columns_axis: $(columns_axis) name: $(name) eltype: $(eltype) overwrite: $(overwrite) {"
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         if !overwrite
             require_no_matrix(daf, rows_axis, columns_axis, name; relayout = false)
@@ -834,8 +834,8 @@ function relayout_matrix!(
     Formats.with_data_write_lock(daf, "relayout_matrix! of:", name, "of:", rows_axis, "and:", columns_axis) do
         @debug "relayout_matrix! daf: $(depict(daf)) rows_axis: $(rows_axis) columns_axis: $(columns_axis) name: $(name) overwrite: $(overwrite) {"
 
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         if rows_axis == columns_axis
             error(
@@ -923,8 +923,8 @@ function delete_matrix!(
         relayout = relayout && rows_axis != columns_axis
         @debug "delete_matrix! daf: $(depict(daf)) rows_axis: $(rows_axis) columns_axis: $(columns_axis) name: $(name) must exist: $(must_exist)"
 
-        require_axis(daf, rows_axis)
-        require_axis(daf, columns_axis)
+        require_axis(daf, "for the rows of the matrix: $(name)", rows_axis)
+        require_axis(daf, "for the columns of the matrix: $(name)", columns_axis)
 
         if must_exist
             require_matrix(daf, rows_axis, columns_axis, name; relayout = relayout)

diff --git a/test/copies.jl b/test/copies.jl
@@ -103,7 +103,8 @@ nested_test("copies") do
         nested_test("missing") do
             @test_throws dedent("""
                 missing axis: cell
-                in the daf data: source!
+                for: axis_array
+                of the daf data: source!
             """) copy_axis!(source = source, destination = destination, axis = "cell")
         end
 
@@ -121,15 +122,17 @@ nested_test("copies") do
             nested_test("()") do
                 @test_throws dedent("""
                     missing axis: cell
-                    in the daf data: destination!
+                    for: axis_array
+                    of the daf data: destination!
                 """) copy_vector!(source = source, destination = destination, axis = "cell", name = "age")
             end
 
             nested_test("default") do
                 nested_test("undef") do
                     @test_throws dedent("""
                         missing axis: cell
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_vector!(
                         source = source,
                         destination = destination,
@@ -142,7 +145,8 @@ nested_test("copies") do
                 nested_test("nothing") do
                     @test_throws dedent("""
                         missing axis: cell
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_vector!(;
                         source = source,
                         destination = destination,
@@ -155,7 +159,8 @@ nested_test("copies") do
                 nested_test("value") do
                     @test_throws dedent("""
                         missing axis: cell
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_vector!(;
                         source = source,
                         destination = destination,
@@ -525,7 +530,8 @@ nested_test("copies") do
             nested_test("()") do
                 @test_throws dedent("""
                     missing axis: cell
-                    in the daf data: destination!
+                    for: axis_array
+                    of the daf data: destination!
                 """) copy_matrix!(
                     source = source,
                     destination = destination,
@@ -538,7 +544,8 @@ nested_test("copies") do
 
                 @test_throws dedent("""
                     missing axis: gene
-                    in the daf data: destination!
+                    for: axis_array
+                    of the daf data: destination!
                 """) copy_matrix!(
                     source = source,
                     destination = destination,
@@ -552,7 +559,8 @@ nested_test("copies") do
                 nested_test("undef") do
                     @test_throws dedent("""
                         missing axis: cell
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_matrix!(
                         source = source,
                         destination = destination,
@@ -566,7 +574,8 @@ nested_test("copies") do
 
                     @test_throws dedent("""
                         missing axis: gene
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_matrix!(
                         source = source,
                         destination = destination,
@@ -580,7 +589,8 @@ nested_test("copies") do
                 nested_test("nothing") do
                     @test_throws dedent("""
                         missing axis: cell
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_matrix!(
                         source = source,
                         destination = destination,
@@ -594,7 +604,8 @@ nested_test("copies") do
 
                     @test_throws dedent("""
                         missing axis: gene
-                        in the daf data: destination!
+                        for: axis_array
+                        of the daf data: destination!
                     """) copy_matrix!(
                         source = source,
                         destination = destination,