Merge remote-tracking branch 'origin/develop'

LCSB-BioCore · Oct 23, 2024 · 8542c3b · 8542c3b
2 parents cf5ba8a + 0f10c31
commit 8542c3b
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Showing 4 changed files with 37 additions and 16 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["The developers of COBREXA.jl"]
-version = "1.5.1"
+version = "1.5.2"
 
 [deps]
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -31,17 +31,17 @@ DistributedData = "0.1.4, 0.2"
 DocStringExtensions = "0.8, 0.9"
 Downloads = "1"
 GLPK = "1"
-HDF5 = "0.16"
+HDF5 = "0.16, 0.17"
 JSON = "0.21"
 JuMP = "1"
 LinearAlgebra = "1"
 MAT = "0.10"
 MacroTools = "0.5.6"
 OrderedCollections = "1.4"
-PikaParser = "0.5"
+PikaParser = "0.5, 0.6"
 Pkg = "1"
 Random = "1"
-SBML = "~1.3, ~1.4"
+SBML = "~1.3, ~1.4, ~1.5"
 SHA = "0.7, 1"
 Serialization = "1"
 SparseArrays = "1"

diff --git a/src/base/types/JSONModel.jl b/src/base/types/JSONModel.jl
@@ -62,8 +62,10 @@ JSONModel(json::Dict{String,Any}) = begin
 end
 
 function _parse_annotations(x)::Annotations
-    Annotations([k => if typeof(v) == String
+    Annotations([k => if v isa String
         [v]
+    elseif v isa AbstractDict
+        string.(collect(v))
     else
         convert(Vector{String}, v)
     end for (k, v) in x])
@@ -161,6 +163,7 @@ Parses the `.gene_reaction_rule` from reactions.
 reaction_gene_association(model::JSONModel, rid::String) = _maybemap(
     _parse_grr,
     get(model.rxns[model.rxn_index[rid]], "gene_reaction_rule", nothing),
+    nothing,
 )
 
 """
@@ -176,8 +179,11 @@ $(TYPEDSIGNATURES)
 
 Parse and return the metabolite `.formula`
 """
-metabolite_formula(model::JSONModel, mid::String) =
-    _maybemap(_parse_formula, get(model.mets[model.met_index[mid]], "formula", nothing))
+metabolite_formula(model::JSONModel, mid::String) = _maybemap(
+    _parse_formula,
+    get(model.mets[model.met_index[mid]], "formula", nothing),
+    nothing,
+)
 
 """
 $(TYPEDSIGNATURES)
@@ -203,15 +209,19 @@ Gene annotations from the [`JSONModel`](@ref).
 gene_annotations(model::JSONModel, gid::String)::Annotations = _maybemap(
     _parse_annotations,
     get(model.genes[model.gene_index[gid]], "annotation", nothing),
+    Annotations(),
 )
 
 """
 $(TYPEDSIGNATURES)
 
 Gene notes from the [`JSONModel`](@ref).
 """
-gene_notes(model::JSONModel, gid::String)::Notes =
-    _maybemap(_parse_notes, get(model.genes[model.gene_index[gid]], "notes", nothing))
+gene_notes(model::JSONModel, gid::String)::Notes = _maybemap(
+    _parse_notes,
+    get(model.genes[model.gene_index[gid]], "notes", nothing),
+    Notes(),
+)
 
 """
 $(TYPEDSIGNATURES)
@@ -221,15 +231,19 @@ Reaction annotations from the [`JSONModel`](@ref).
 reaction_annotations(model::JSONModel, rid::String)::Annotations = _maybemap(
     _parse_annotations,
     get(model.rxns[model.rxn_index[rid]], "annotation", nothing),
+    Annotations(),
 )
 
 """
 $(TYPEDSIGNATURES)
 
 Reaction notes from the [`JSONModel`](@ref).
 """
-reaction_notes(model::JSONModel, rid::String)::Notes =
-    _maybemap(_parse_notes, get(model.rxns[model.rxn_index[rid]], "notes", nothing))
+reaction_notes(model::JSONModel, rid::String)::Notes = _maybemap(
+    _parse_notes,
+    get(model.rxns[model.rxn_index[rid]], "notes", nothing),
+    Notes(),
+)
 
 """
 $(TYPEDSIGNATURES)
@@ -239,15 +253,19 @@ Metabolite annotations from the [`JSONModel`](@ref).
 metabolite_annotations(model::JSONModel, mid::String)::Annotations = _maybemap(
     _parse_annotations,
     get(model.mets[model.met_index[mid]], "annotation", nothing),
+    Annotations(),
 )
 
 """
 $(TYPEDSIGNATURES)
 
 Metabolite notes from the [`JSONModel`](@ref).
 """
-metabolite_notes(model::JSONModel, mid::String)::Notes =
-    _maybemap(_parse_notes, get(model.mets[model.met_index[mid]], "notes", nothing))
+metabolite_notes(model::JSONModel, mid::String)::Notes = _maybemap(
+    _parse_notes,
+    get(model.mets[model.met_index[mid]], "notes", nothing),
+    Notes(),
+)
 
 """
 $(TYPEDSIGNATURES)

diff --git a/src/base/types/abstract/Maybe.jl b/src/base/types/abstract/Maybe.jl
@@ -18,8 +18,9 @@ end
 """
 $(TYPEDSIGNATURES)
 
-Apply a function to `x` only if it is not `nothing`.
+Apply a function to `x` only if it is not `nothing`. Returns `f(x)` when
+applied, otherwise returns `default`.
 """
-function _maybemap(f, x::Maybe)::Maybe
-    isnothing(x) ? nothing : f(x)
+function _maybemap(f, x::Maybe, default = nothing)::Maybe
+    isnothing(x) ? default : f(x)
 end
diff --git a/src/base/utils/gene_associations.jl b/src/base/utils/gene_associations.jl
@@ -95,6 +95,8 @@ const _grr_grammar = begin
         x == '-' ||
         x == ':' ||
         x == '.' ||
+        x == '@' ||
+        x == '#' ||
         x == '\'' ||
         x == '[' ||
         x == ']' ||