add support for groups extension

Project.toml

@@ -1,7 +1,7 @@
 name = "SBML"
 uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
 authors = ["Mirek Kratochvil <[email protected]>", "LCSB R3 team <[email protected]>"]
-version = "1.5.1"
+version = "1.6"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -16,7 +16,7 @@ ConstructionBase = "1.3"
 DocStringExtensions = "0.8, 0.9"
 IfElse = "0.1"
 SBML_jll = "5.19.5"
-Symbolics = "3, 4"
+Symbolics = "5"
 Unitful = "1"
 julia = "1.6"
 

src/readsbml.jl

@@ -252,6 +252,7 @@ readSBMLFromString(
 
 get_notes(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getNotesString)
 get_annotation(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getAnnotationString)
+get_metaid(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getMetaId)
 
 """
 $(TYPEDSIGNATURES)
@@ -293,7 +294,7 @@ get_parameter(p::VPtr)::Pair{String,Parameter} =
         value = get_optional_double(p, :Parameter_isSetValue, :Parameter_getValue),
         units = get_optional_string(p, :Parameter_getUnits),
         constant = get_optional_bool(p, :Parameter_isSetConstant, :Parameter_getConstant),
-        metaid = get_optional_string(p, :SBase_getMetaId),
+        metaid = get_metaid(p),
         notes = get_notes(p),
         annotation = get_annotation(p),
         sbo = get_sbo_term(p),
@@ -309,6 +310,8 @@ valid [`SBML.Model`](@ref) structure.
 function get_model(mdl::VPtr)::SBML.Model
     # get the FBC plugin pointer (FbcModelPlugin_t)
     mdl_fbc = ccall(sbml(:SBase_getPlugin), VPtr, (VPtr, Cstring), mdl, "fbc")
+    # and the Groups plugin pointer (GroupModelPlugin_t)
+    mdl_groups = ccall(sbml(:SBase_getPlugin), VPtr, (VPtr, Cstring), mdl, "groups")
 
     # get the parameters
     parameters = Dict{String,Parameter}()
@@ -364,7 +367,7 @@ function get_model(mdl::VPtr)::SBML.Model
             ),
             size = get_optional_double(co, :Compartment_isSetSize, :Compartment_getSize),
             units = get_optional_string(co, :Compartment_getUnits),
-            metaid = get_optional_string(co, :SBase_getMetaId),
+            metaid = get_metaid(co),
             notes = get_notes(co),
             annotation = get_annotation(co),
             sbo = get_sbo_term(co),
@@ -423,7 +426,7 @@ function get_model(mdl::VPtr)::SBML.Model
                 :Species_getHasOnlySubstanceUnits,
             ),
             constant = get_optional_bool(sp, :Species_isSetConstant, :Species_getConstant),
-            metaid = get_optional_string(sp, :SBase_getMetaId),
+            metaid = get_metaid(sp),
             notes = get_notes(sp),
             annotation = get_annotation(sp),
             sbo = get_sbo_term(sp),
@@ -567,7 +570,7 @@ function get_model(mdl::VPtr)::SBML.Model
             gene_product_association = association,
             kinetic_math = math,
             reversible,
-            metaid = get_optional_string(re, :SBase_getMetaId),
+            metaid = get_metaid(re),
             notes = get_notes(re),
             annotation = get_annotation(re),
             sbo = get_sbo_term(re),
@@ -593,7 +596,7 @@ function get_model(mdl::VPtr)::SBML.Model
                 gene_products[id] = GeneProduct(
                     label = get_string(gp, :GeneProduct_getLabel),
                     name = get_optional_string(gp, :GeneProduct_getName),
-                    metaid = get_optional_string(gp, :SBase_getMetaId),
+                    metaid = get_metaid(gp),
                     notes = get_notes(gp),
                     annotation = get_annotation(gp),
                     sbo = get_sbo_term(gp),
@@ -614,7 +617,7 @@ function get_model(mdl::VPtr)::SBML.Model
         function_definitions[get_string(fd, :FunctionDefinition_getId)] =
             FunctionDefinition(
                 name = get_optional_string(fd, :FunctionDefinition_getName),
-                metaid = get_optional_string(fd, :SBase_getMetaId),
+                metaid = get_metaid(fd),
                 body = def,
                 notes = get_notes(fd),
                 annotation = get_annotation(fd),
@@ -625,8 +628,8 @@ function get_model(mdl::VPtr)::SBML.Model
 
     initial_assignments = Dict{String,Math}()
     num_ias = ccall(sbml(:Model_getNumInitialAssignments), Cuint, (VPtr,), mdl)
-    for n = 0:(num_ias-1)
-        ia = ccall(sbml(:Model_getInitialAssignment), VPtr, (VPtr, Cuint), mdl, n)
+    for i = 0:(num_ias-1)
+        ia = ccall(sbml(:Model_getInitialAssignment), VPtr, (VPtr, Cuint), mdl, i)
         sym = ccall(sbml(:InitialAssignment_getSymbol), Cstring, (VPtr,), ia)
         math_ptr = ccall(sbml(:InitialAssignment_getMath), VPtr, (VPtr,), ia)
         if math_ptr != C_NULL
@@ -637,8 +640,8 @@ function get_model(mdl::VPtr)::SBML.Model
     # events
     events = Pair{Maybe{String},Event}[]
     num_events = ccall(sbml(:Model_getNumEvents), Cuint, (VPtr,), mdl)
-    for n = 0:(num_events-1)
-        ev = ccall(sbml(:Model_getEvent), VPtr, (VPtr, Cuint), mdl, n)
+    for i = 0:(num_events-1)
+        ev = ccall(sbml(:Model_getEvent), VPtr, (VPtr, Cuint), mdl, i)
 
         event_assignments = EventAssignment[]
         for j = 0:(ccall(sbml(:Event_getNumEventAssignments), Cuint, (VPtr,), ev)-1)
@@ -684,11 +687,11 @@ function get_model(mdl::VPtr)::SBML.Model
         )
     end
 
-    # Rules
+    # rules
     rules = Rule[]
     num_rules = ccall(sbml(:Model_getNumRules), Cuint, (VPtr,), mdl)
-    for n = 0:(num_rules-1)
-        rule_ptr = ccall(sbml(:Model_getRule), VPtr, (VPtr, Cuint), mdl, n)
+    for i = 0:(num_rules-1)
+        rule_ptr = ccall(sbml(:Model_getRule), VPtr, (VPtr, Cuint), mdl, i)
         type = if ccall(sbml(:Rule_isAlgebraic), Bool, (VPtr,), rule_ptr)
             AlgebraicRule
         elseif ccall(sbml(:Rule_isAssignment), Bool, (VPtr,), rule_ptr)
@@ -711,11 +714,11 @@ function get_model(mdl::VPtr)::SBML.Model
         end
     end
 
-    # Constraints
+    # constraints
     constraints = Constraint[]
     num_constraints = ccall(sbml(:Model_getNumConstraints), Cuint, (VPtr,), mdl)
-    for n = 0:(num_constraints-1)
-        constraint_ptr = ccall(sbml(:Model_getConstraint), VPtr, (VPtr, Cuint), mdl, n)
+    for i = 0:(num_constraints-1)
+        constraint_ptr = ccall(sbml(:Model_getConstraint), VPtr, (VPtr, Cuint), mdl, i)
         xml_ptr = ccall(sbml(:Constraint_getMessage), VPtr, (VPtr,), constraint_ptr)
         message = get_string_from_xmlnode(xml_ptr)
         math_ptr = ccall(sbml(:Constraint_getMath), VPtr, (VPtr,), constraint_ptr)
@@ -726,6 +729,44 @@ function get_model(mdl::VPtr)::SBML.Model
         end
     end
 
+    # groups (these require the groups extension)
+    groups = Dict{String,Group}()
+    if mdl_groups != C_NULL
+        num_groups =
+            ccall(sbml(:GroupsModelPlugin_getNumGroups), Cuint, (VPtr,), mdl_groups)
+        for i = 0:(num_groups-1)
+            grp =
+                ccall(sbml(:GroupsModelPlugin_getGroup), VPtr, (VPtr, Cuint), mdl_groups, i)
+            members = Member[
+                let mem = ccall(sbml(:Group_getMember), VPtr, (VPtr, Cuint), grp, mi)
+                    Member(;
+                        id = get_optional_string(mem, :Member_getId),
+                        metaid = get_metaid(mem),
+                        name = get_optional_string(mem, :Member_getName),
+                        id_ref = get_optional_string(mem, :Member_getIdRef),
+                        metaid_ref = get_optional_string(mem, :Member_getMetaIdRef),
+                        notes = get_notes(mem),
+                        annotation = get_annotation(mem),
+                        sbo = get_sbo_term(mem),
+                        cv_terms = get_cv_terms(mem),
+                    )
+                end for
+                mi = 0:(ccall(sbml(:Group_getNumMembers), Cuint, (VPtr,), grp)-1)
+            ]
+
+            groups[get_string(grp, :Group_getId)] = Group(;
+                metaid = get_metaid(grp),
+                kind = get_optional_string(grp, :Group_getKindAsString),
+                name = get_optional_string(grp, :Group_getName),
+                members,
+                notes = get_notes(grp),
+                annotation = get_annotation(grp),
+                sbo = get_sbo_term(grp),
+                cv_terms = get_cv_terms(grp),
+            )
+        end
+    end
+
     return Model(;
         parameters,
         units,
@@ -742,7 +783,7 @@ function get_model(mdl::VPtr)::SBML.Model
         events,
         name = get_optional_string(mdl, :Model_getName),
         id = get_optional_string(mdl, :Model_getId),
-        metaid = get_optional_string(mdl, :SBase_getMetaId),
+        metaid = get_metaid(mdl),
         conversion_factor = get_optional_string(mdl, :Model_getConversionFactor),
         area_units = get_optional_string(mdl, :Model_getAreaUnits),
         extent_units = get_optional_string(mdl, :Model_getExtentUnits),

src/structs.jl

@@ -450,6 +450,41 @@ end
 """
 $(TYPEDEF)
 
+# Fields
+$(TYPEDFIELDS)
+"""
+Base.@kwdef struct Member
+    id::Maybe{String} = nothing
+    metaid::Maybe{String} = nothing
+    name::Maybe{String} = nothing
+    id_ref::Maybe{String} = nothing
+    metaid_ref::Maybe{String} = nothing
+    notes::Maybe{String} = nothing
+    annotation::Maybe{String} = nothing
+    sbo::Maybe{String} = nothing
+    cv_terms::Vector{CVTerm} = []
+end
+
+"""
+$(TYPEDEF)
+
+# Fields
+$(TYPEDFIELDS)
+"""
+Base.@kwdef struct Group
+    metaid::Maybe{String} = nothing
+    kind::Maybe{String} = nothing
+    name::Maybe{String} = nothing
+    members::Vector{Member} = []
+    notes::Maybe{String} = nothing
+    annotation::Maybe{String} = nothing
+    sbo::Maybe{String} = nothing
+    cv_terms::Vector{CVTerm} = []
+end
+
+"""
+$(TYPEDEF)
+
 Structure that collects the model-related data. Contains `parameters`, `units`,
 `compartments`, `species` and `reactions` and `gene_products`, and additional
 `notes` and `annotation` (also present internally in some of the data fields).
@@ -473,6 +508,7 @@ Base.@kwdef struct Model
     gene_products::Dict{String,GeneProduct} = Dict()
     function_definitions::Dict{String,FunctionDefinition} = Dict()
     events::Vector{Pair{Maybe{String},Event}} = Pair{Maybe{String},Event}[]
+    groups::Dict{String,Group} = Dict()
     name::Maybe{String} = nothing
     id::Maybe{String} = nothing
     metaid::Maybe{String} = nothing