Merge pull request #62 from LCSB-BioCore/mk-frog-012

update the frog report format to 0.1.2
LCSB-BioCore · Mar 24, 2023 · d39868b · d39868b · exaexa · Mar 25, 2023
2 parents 4d90b43 + 54f25ff
commit d39868b
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Showing 5 changed files with 75 additions and 27 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,10 +1,11 @@
 name = "FBCModelTests"
 uuid = "1060cd45-1c33-4a14-be81-8fa38fdd82bf"
 authors = ["The developers of FBCModelTests.jl"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 COBREXA = "babc4406-5200-4a30-9033-bf5ae714c842"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

diff --git a/src/frog/io.jl b/src/frog/io.jl
@@ -129,7 +129,8 @@ function load_report(
         FROGMetadata(JSON.parse(f))
     end
 
-    basefilename = metadata["model.filename"]
+    basefilename = get(metadata, "model_filename", get(metadata, "model.filename", nothing))
+    isnothing(basefilename) && error("report does not list its filename")
 
     # objectives
     objdata = readfrom("01_objective.tsv") do f

diff --git a/src/frog/report.jl b/src/frog/report.jl
@@ -12,6 +12,7 @@ using ...FBCModelTests: FBCMT_VERSION
 
 using COBREXA
 using JuMP
+using Dates
 using Distributed
 using DocStringExtensions
 using MD5
@@ -157,18 +158,35 @@ $(TYPEDSIGNATURES)
 """
 generate_metadata(filename::String; optimizer, basefilename::String = basename(filename)) =
     FROGMetadata(
-        "software.name" => "FBCModelTests.jl",
-        "software.version" => string(FBCMT_VERSION),
-        "software.url" => "https://github.com/LCSB-BioCore/FBCModelTests.jl/",
+        "frog_version" => "0.1.2",
+        "frog_date" => string(Dates.today()),
+        "model_filename" => basefilename,
+        "model_md5" => bytes2hex(open(f -> md5(f), filename, "r")),
+        "model_sha256" => bytes2hex(open(f -> sha256(f), filename, "r")),
         "environment" => begin
             x = IOBuffer()
             InteractiveUtils.versioninfo(x)
             replace(String(take!(x)), r"\n *" => " ")
         end,
-        "model.filename" => basefilename,
-        "model.md5" => bytes2hex(open(f -> md5(f), filename, "r")),
-        "model.sha256" => bytes2hex(open(f -> sha256(f), filename, "r")),
-        "solver.name" => "COBREXA.jl $COBREXA_VERSION ($(COBREXA.JuMP.MOI.get(optimizer(), COBREXA.JuMP.MOI.SolverName())))",
+        "software" => Dict(
+            "frog" => Dict(
+                "name" => "FBCModelTests.jl",
+                "version" => string(FBCMT_VERSION),
+                "url" => "https://github.com/LCSB-BioCore/FBCModelTests.jl",
+            ),
+            "toolbox" => Dict(
+                "name" => "COBREXA.jl",
+                "version" => string(COBREXA_VERSION),
+                "url" => "https://github.com/LCSB-BioCore/COBREXA.jl",
+            ),
+            "solver" => Dict(
+                "name" => COBREXA.JuMP.MOI.get(optimizer(), COBREXA.JuMP.MOI.SolverName()),
+                "version" => COBREXA.JuMP.MOI.get(
+                    optimizer(),
+                    COBREXA.JuMP.MOI.SolverVersion(),
+                ),
+            ),
+        ),
     )
 
 end
@@ -238,14 +256,14 @@ end
 $(TYPEDSIGNATURES)
 """
 function test_metadata_compatibility(a::FROGMetadata, b::FROGMetadata)
-    for k in ["model.filename", "model.md5"]
+    for k in ["model_filename", "model_md5"]
         @testset "$k is present" begin
             @test haskey(a, k)
             @test haskey(b, k)
         end
     end
 
-    for k in ["model.filename", "model.md5", "model.sha256"]
+    for k in ["model_filename", "model_md5", "model_sha256"]
         if haskey(a, k) && haskey(b, k)
             @testset "$k matches" begin
                 @test a[k] == b[k]

diff --git a/test/data/report-ecoli-damaged/metadata.json b/test/data/report-ecoli-damaged/metadata.json
@@ -1,10 +1,24 @@
 {
-  "model.sha256": "b4db506aeed0e434c1f5f0fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
-  "model.md5": "4574760460afe9e1b3388dc16f354706",
-  "software.name": "FBCModelTests.jl",
-  "environment": "Julia Version 1.9.0-beta2 Commit 7daffeecb8c (2022-12-29 07:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) CPU: 16 × Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-14.0.6 (ORCJIT, skylake) Threads: 1 on 16 virtual cores Environment: JULIA_LOAD_PATH = @:/tmp/jl_acZx63 ",
-  "software.version": "0.1.0",
-  "software.url": "https://github.com/LCSB-BioCore/FBCModelTests.jl/",
-  "model.filename": "e_coli_core.xml",
-  "solver.name": "COBREXA.jl 1.4.3 (GLPK)"
+  "software": {
+    "frog": {
+      "name": "FBCModelTests.jl",
+      "version": "0.2.1",
+      "url": "https://github.com/LCSB-BioCore/FBCModelTests.jl"
+    },
+    "toolbox": {
+      "name": "COBREXA.jl",
+      "version": "1.4.4",
+      "url": "https://github.com/LCSB-BioCore/COBREXA.jl"
+    },
+    "solver": {
+      "name": "GLPK",
+      "version": "5.0"
+    }
+  },
+  "model_filename": "e_coli_core.xml",
+  "frog_date": "2023-03-24",
+  "model_sha256": "b4db506aeed0e434c1f5f0fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
+  "model_md5": "4574760460afe9e1b3388dc16f354706",
+  "environment": "Julia Version 1.9.0-beta3 Commit 24204a73447 (2023-01-18 07:20 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) CPU: 8 × AMD Ryzen 7 2700U with Radeon Vega Mobile Gfx WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-14.0.6 (ORCJIT, znver1) Threads: 1 on 8 virtual cores Environment: JULIA_LOAD_PATH = @:/tmp/jl_icHaNw ",
+  "frog_version": "0.1.2"
 }
diff --git a/test/data/report-ecoli-good/metadata.json b/test/data/report-ecoli-good/metadata.json
@@ -1,10 +1,24 @@
 {
-  "model.sha256": "b4db506aeed0e434c1f5f1fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
-  "model.md5": "4574760460afe9e1b3388dc15f354706",
-  "software.name": "FBCModelTests.jl",
-  "environment": "Julia Version 1.9.0-beta2 Commit 7daffeecb8c (2022-12-29 07:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) CPU: 16 × Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-14.0.6 (ORCJIT, skylake) Threads: 1 on 16 virtual cores Environment: JULIA_LOAD_PATH = @:/tmp/jl_acZx63 ",
-  "software.version": "0.1.0",
-  "software.url": "https://github.com/LCSB-BioCore/FBCModelTests.jl/",
-  "model.filename": "e_coli_core.xml",
-  "solver.name": "COBREXA.jl 1.4.3 (GLPK)"
+  "software": {
+    "frog": {
+      "name": "FBCModelTests.jl",
+      "version": "0.2.1",
+      "url": "https://github.com/LCSB-BioCore/FBCModelTests.jl"
+    },
+    "toolbox": {
+      "name": "COBREXA.jl",
+      "version": "1.4.4",
+      "url": "https://github.com/LCSB-BioCore/COBREXA.jl"
+    },
+    "solver": {
+      "name": "GLPK",
+      "version": "5.0"
+    }
+  },
+  "model_filename": "e_coli_core.xml",
+  "frog_date": "2023-03-24",
+  "model_sha256": "b4db506aeed0e434c1f5f1fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
+  "model_md5": "4574760460afe9e1b3388dc15f354706",
+  "environment": "Julia Version 1.9.0-beta3 Commit 24204a73447 (2023-01-18 07:20 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) CPU: 8 × AMD Ryzen 7 2700U with Radeon Vega Mobile Gfx WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-14.0.6 (ORCJIT, znver1) Threads: 1 on 8 virtual cores Environment: JULIA_LOAD_PATH = @:/tmp/jl_icHaNw ",
+  "frog_version": "0.1.2"
 }