Merge pull request #117 from LCSB-BioCore/mk-error-severities

handle SBML error severities (and don't throw on warnings)

src/readsbml.jl

@@ -72,7 +72,11 @@ function get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
 end
 
 """
-    function readSBML(fn::String, sbml_conversion = model->nothing)::SBML.Model
+    readSBML(
+        fn::String,
+        sbml_conversion = document -> nothing;
+        report_severities = ["Fatal", "Error"],
+    )::SBML.Model
 
 Read the SBML from a XML file in `fn` and return the contained `SBML.Model`.
 
@@ -82,6 +86,9 @@ single parameter, which is the C pointer to the loaded SBML document (C type
 [`set_level_and_version`](@ref), [`libsbml_convert`](@ref), and
 [`convert_simplify_math`](@ref).
 
+`report_severities` switches on and off reporting of certain errors; see the
+documentation of [`get_error_messages`](@ref) for details.
+
 # Example
 ```
 m = readSBML("my_model.xml", doc -> begin
@@ -90,10 +97,18 @@ m = readSBML("my_model.xml", doc -> begin
 end)
 ```
 """
-function readSBML(fn::String, sbml_conversion = document -> nothing)::SBML.Model
+function readSBML(
+    fn::String,
+    sbml_conversion = document -> nothing;
+    report_severities = ["Fatal", "Error"],
+)::SBML.Model
     doc = ccall(sbml(:readSBML), VPtr, (Cstring,), fn)
     try
-        get_error_messages(doc, AssertionError("Opening SBML document has reported errors"))
+        get_error_messages(
+            doc,
+            AssertionError("Opening SBML document has reported errors"),
+            report_severities,
+        )
 
         sbml_conversion(doc)
 

src/utils.jl

@@ -148,26 +148,45 @@ function extensive_kinetic_math(
 end
 
 """
-    get_error_messages(doc::Ptr{Cvoid}, error::Exception)
+    get_error_messages(doc::VPtr, error::Exception, report_severities)
 
 Show the error messages reported by SBML in the `doc` document and throw the
 `error` if they are more than 1.
+
+`report_severities` switches the reporting of certain error types defined by
+libsbml; you can choose from `["Fatal", "Error", "Warning", "Informational"]`.
 """
-function get_error_messages(doc::VPtr, error::Exception)
+function get_error_messages(doc::VPtr, error::Exception, report_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)))
-        @error "SBML reported error: $(msg)"
-    end
-    if n_errs > 0
-        throw(error)
+        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
     end
+    do_throw && throw(error)
     nothing
 end
 
 """
-    check_errors(success::Integer, doc::Ptr{Cvoid}, error::Exception)
+    check_errors(
+        success::Integer,
+        doc::VPtr,
+        error::Exception,
+        report_severities = ["Fatal", "Error"],
+    )
 
 If success is a 0-valued `Integer` (a logical `false`), then call
 [`get_error_messages`](@ref) to show the error messages reported by SBML in the
@@ -175,5 +194,9 @@ If success is a 0-valued `Integer` (a logical `false`), then call
 typically the value returned by an SBML C function operating on `doc` which
 returns a boolean flag to signal a successful operation.
 """
-check_errors(success::Integer, doc::VPtr, error::Exception) =
-    Bool(success) || get_error_messages(doc, error)
+check_errors(
+    success::Integer,
+    doc::VPtr,
+    error::Exception,
+    report_severities = ["Fatal", "Error"],
+) = Bool(success) || get_error_messages(doc, error, report_severities)