Merge pull request #123 from giordano/mg/read-from-string

Add function to read SBML model from a string

src/SBML.jl

@@ -18,7 +18,7 @@ include("utils.jl")
 
 sbml(sym::Symbol) = dlsym(SBML_jll.libsbml_handle, sym)
 
-export readSBML, getS, getLBs, getUBs, getOCs
+export readSBML, readSBMLFromString, getS, getLBs, getUBs, getOCs
 export set_level_and_version, libsbml_convert, convert_simplify_math
 
 end # module

src/readsbml.jl

@@ -71,6 +71,34 @@ function get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
     end
 end
 
+function _readSBML(
+    symbol::Symbol,
+    fn::String,
+    sbml_conversion,
+    report_severities,
+)::SBML.Model
+    doc = ccall(sbml(symbol), VPtr, (Cstring,), fn)
+    try
+        get_error_messages(
+            doc,
+            AssertionError("Opening SBML document has reported errors"),
+            report_severities,
+        )
+
+        sbml_conversion(doc)
+
+        if 0 == ccall(sbml(:SBMLDocument_isSetModel), Cint, (VPtr,), doc)
+            throw(AssertionError("SBML document contains no model"))
+        end
+
+        model = ccall(sbml(:SBMLDocument_getModel), VPtr, (VPtr,), doc)
+
+        return extractModel(model)
+    finally
+        ccall(sbml(:SBMLDocument_free), Nothing, (VPtr,), doc)
+    end
+end
+
 """
     readSBML(
         fn::String,
@@ -89,6 +117,8 @@ single parameter, which is the C pointer to the loaded SBML document (C type
 `report_severities` switches 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).
+
 # Example
 ```
 m = readSBML("my_model.xml", doc -> begin
@@ -97,32 +127,29 @@ m = readSBML("my_model.xml", doc -> begin
 end)
 ```
 """
-function readSBML(
+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"),
-            report_severities,
-        )
+)::SBML.Model = _readSBML(:readSBML, fn, sbml_conversion, report_severities)
 
-        sbml_conversion(doc)
-
-        if 0 == ccall(sbml(:SBMLDocument_isSetModel), Cint, (VPtr,), doc)
-            throw(AssertionError("SBML document contains no model"))
-        end
+"""
+    readSBML(
+        str::String,
+        sbml_conversion = document -> nothing;
+        report_severities = ["Fatal", "Error"],
+    )::SBML.Model
 
-        model = ccall(sbml(:SBMLDocument_getModel), VPtr, (VPtr,), doc)
+Read the SBML from the string `str` and return the contained `SBML.Model`.
 
-        return extractModel(model)
-    finally
-        ccall(sbml(:SBMLDocument_free), Nothing, (VPtr,), doc)
-    end
-end
+For the other arguments see the docstring of [`readSBML`](@ref), which can be
+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)
 
 get_notes(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getNotesString)
 get_annotation(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getAnnotationString)

test/loadmodels.jl

@@ -74,7 +74,7 @@ sbmlfiles = [
     ),
 ]
 
-@testset "Loading of models from various sources" begin
+@testset "Loading of models from various sources - $(reader)" for reader in (readSBML,  readSBMLFromString)
     for (sbmlfile, url, hash, expected_mets, expected_rxns) in sbmlfiles
         if !isfile(sbmlfile)
             Downloads.download(url, sbmlfile)
@@ -86,7 +86,11 @@ sbmlfiles = [
         end
 
         @testset "Loading of $sbmlfile" begin
-            mdl = readSBML(sbmlfile)
+            mdl = if reader === readSBML
+                readSBML(sbmlfile)
+            else
+                readSBMLFromString(readchomp(sbmlfile))
+            end
 
             @test typeof(mdl) == Model
 
@@ -98,6 +102,10 @@ sbmlfiles = [
     end
 end
 
+@testset "readSBMLFromString" begin
+    @test_logs (:error, r"^SBML reported error") @test_throws AssertionError readSBMLFromString("")
+end
+
 @testset "Time variables in math" begin
     # this test is here mainly for keeping a magical constant that we need for
     # parsing time synced with libsbml source