Merge pull request #243 from LCSB-BioCore/mk-softer-error-reporting

make throwing SBML load errors configurable
LCSB-BioCore · Jan 31, 2023 · 89a29d8 · 89a29d8
2 parents d174aed + 630b4aa
commit 89a29d8
Show file tree

Hide file tree

Showing 2 changed files with 30 additions and 11 deletions.
diff --git a/src/readsbml.jl b/src/readsbml.jl
@@ -173,13 +173,15 @@ function _readSBML(
     fn::String,
     sbml_conversion,
     report_severities,
+    throw_severities,
 )::SBML.Model
     doc = ccall(sbml(symbol), VPtr, (Cstring,), fn)
     try
         get_error_messages(
             doc,
             AssertionError("Opening SBML document has reported errors"),
             report_severities,
+            throw_severities,
         )
 
         sbml_conversion(doc)
@@ -207,8 +209,9 @@ single parameter, which is the C pointer to the loaded SBML document (C type
 [`set_level_and_version`](@ref), [`libsbml_convert`](@ref),
 [`convert_simplify_math`](@ref) and [`convert_promotelocals_expandfuns`](@ref).
 
-`report_severities` switches on and off reporting of certain errors; see the
-documentation of [`get_error_messages`](@ref) for details.
+`report_severities` and `throw_severities` switch on and off reporting of
+certain errors; see the documentation of [`get_error_messages`](@ref) for
+details.
 
 To read from a string instead of a file, use [`readSBMLFromString`](@ref).
 
@@ -223,10 +226,11 @@ end)
 function readSBML(
     fn::String,
     sbml_conversion = document -> nothing;
-    report_severities = ["Fatal", "Error"],
+    report_severities = ["Error"],
+    throw_severities = ["Fatal"],
 )::SBML.Model
     isfile(fn) || throw(AssertionError("$(fn) is not a file"))
-    _readSBML(:readSBML, fn, sbml_conversion, report_severities)
+    _readSBML(:readSBML, fn, sbml_conversion, report_severities, throw_severities)
 end
 
 """
@@ -240,9 +244,15 @@ used to read from a file instead of a string.
 readSBMLFromString(
     str::AbstractString,
     sbml_conversion = document -> nothing;
-    report_severities = ["Fatal", "Error"],
-)::SBML.Model =
-    _readSBML(:readSBMLFromString, String(str), sbml_conversion, report_severities)
+    report_severities = ["Error"],
+    throw_severities = ["Fatal"],
+)::SBML.Model = _readSBML(
+    :readSBMLFromString,
+    String(str),
+    sbml_conversion,
+    report_severities,
+    throw_severities,
+)
 
 get_notes(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getNotesString)
 get_annotation(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getAnnotationString)

diff --git a/src/utils.jl b/src/utils.jl
@@ -367,26 +367,34 @@ Show the error messages reported by SBML in the `doc` document and throw the
 
 `report_severities` switches the reporting of certain error types defined by
 libsbml; you can choose from `["Fatal", "Error", "Warning", "Informational"]`.
+
+`throw_severities` selects errors on which the functions throws the `error`.
 """
-function get_error_messages(doc::VPtr, error::Exception, report_severities)
+function get_error_messages(
+    doc::VPtr,
+    error::Exception,
+    report_severities,
+    throw_severities,
+)
     n_errs = ccall(sbml(:SBMLDocument_getNumErrors), Cuint, (VPtr,), doc)
     do_throw = false
     for i = 1:n_errs
         err = ccall(sbml(:SBMLDocument_getError), VPtr, (VPtr, Cuint), doc, i - 1)
         msg = string(strip(get_string(err, :XMLError_getMessage)))
         sev = string(strip(get_string(err, :XMLError_getSeverityAsString)))
+
         # keywords from `libsbml/src/sbml/xml/XMLError.cpp` xmlSeverityStringTable:
         if sev == "Fatal"
             sev in report_severities && @error "SBML reported fatal error: $(msg)"
-            do_throw = true
         elseif sev == "Error"
             sev in report_severities && @error "SBML reported error: $(msg)"
-            do_throw = true
         elseif sev == "Warning"
             sev in report_severities && @warn "SBML reported warning: $(msg)"
         elseif sev == "Informational"
             sev in report_severities && @info "SBML reported: $(msg)"
         end
+
+        sev in throw_severities && (do_throw = true)
     end
     do_throw && throw(error)
     nothing
@@ -406,7 +414,8 @@ check_errors(
     doc::VPtr,
     error::Exception,
     report_severities = ["Fatal", "Error"],
-) = Bool(success) || get_error_messages(doc, error, report_severities)
+    throw_severities = ["Fatal", "Error"],
+) = Bool(success) || get_error_messages(doc, error, report_severities, throw_severities)
 
 """
 $(TYPEDSIGNATURES)