From b5f2b8ec47d18c883d79f096a8054835bc5cb1a0 Mon Sep 17 00:00:00 2001 From: Ivan Date: Fri, 10 Jul 2020 17:54:25 +0300 Subject: [PATCH] updated API (results file, backend, etc), documentation, tests --- README.md | 77 +- SBMLCases/Project.toml | 5 - cases.json | 65634 +++++++++++++++++++++++++++++- cases/output/00004.csv | 104 +- cases/output/00005.csv | 102 +- cases/output/00006.csv | 2 +- cases/output/00007.csv | 102 +- cases/output/00008.csv | 102 +- cases/output/00010.csv | 102 +- cases/output/00011.csv | 100 +- cases/output/00012.csv | 102 +- cases/output/00013.csv | 102 +- cases/output/00014.csv | 102 +- cases/output/00015.csv | 100 +- cases/output/00016.csv | 102 +- cases/output/00017.csv | 102 +- cases/output/00018.csv | 102 +- cases/output/00019.csv | 102 +- cases/output/00020.csv | 100 +- cases/output/00021.csv | 102 +- cases/output/00022.csv | 100 +- cases/output/00023.csv | 102 +- cases/output/00024.csv | 100 +- cases/output/00025.csv | 100 +- cases/output/00027.csv | 100 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+++++++++++++++++++++++++++++++ src/SBMLCases.jl | 373 +- test/runtests.jl | 5 + 121 files changed, 137487 insertions(+), 4508 deletions(-) delete mode 100644 SBMLCases/Project.toml create mode 100644 cases/output/00072.csv create mode 100644 cases/output/00118.csv create mode 100644 cases/output/00195.csv create mode 100644 cases/output/00275.csv create mode 100644 cases/output/00281.csv create mode 100644 cases/output/00516.csv create mode 100644 cases/output/00517.csv create mode 100644 cases/output/00528.csv create mode 100644 cases/output/00604.csv create mode 100644 cases/output/00632.csv create mode 100644 cases/output/00658.csv create mode 100644 cases/output/00659.csv create mode 100644 cases/output/00832.csv create mode 100644 cases/output/00854.csv create mode 100644 cases/output/00898.csv create mode 100644 cases/output/00928.csv create mode 100644 cases/output/00929.csv create mode 100644 cases/output/00976.csv create mode 100644 cases/output/00977.csv create mode 100644 cases/output/00998.csv create mode 100644 cases/output/01018.csv create mode 100644 cases/output/01024.csv create mode 100644 cases/output/01048.csv create mode 100644 cases/output/01061.csv create mode 100644 cases/output/01065.csv create mode 100644 cases/output/01068.csv create mode 100644 cases/output/01079.csv create mode 100644 cases/output/01110.csv create mode 100644 docs/Tag definitions marks.xls create mode 100644 heta/index.heta create mode 100644 heta/table.xlsx create mode 100644 heta/table1.xlsx create mode 100644 heta/~$table.xlsx create mode 100644 results.json diff --git a/README.md b/README.md index 36d0d3e3a..41382b75f 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,78 @@ # SBMLCases -The package replaces SBML Runner application in order to run SBML suite simulations in Julia +The package is designed to test Simulation Software against [SBML Test Suite Cases](https://github.com/sbmlteam/sbml-test-suite) in Julia. + +## Overview + +SBMLCases.jl contains: +- [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite) cases in `cases_path = "./cases/semantic"`. The original Matlab models were converted to Julia with Heta compiler. Julia code for each model is stored in `./cases/semantic//julia`, while models' settings and tags are stored in `cases_db = "./cases.json"`. +- API (documented in the *Usage* section) to upload `cases_db`, run simulations, save results to `output_path = "./cases/output"` and update status in `results_db = "./results.json"`. A simulation can end with one of the three status: `success` indicates the output file has passed tolerance test, `failure` signifies that tolerance test for a given simulation was not passed and `error` stand for any error during the simulation (error message is printed to the `message` field in `results_db`). + +Currently SBMLCases.jl suport only one `SimSolver` Simulation Backend. + +## Usage + +SBMLCases.jl exports the following functions: + +``` + upload_cases(;json::AbstractString=cases_db) + +Upload cases from `cases_db`. +``` + +``` + add_cases(; + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db + ) + +Add new cases from `cases_path` to `cases_db`. +``` + +``` + update_results( + case::AbstractString, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) + +Reads `cases_db` to `cases_dict`, accesses the `case`, +solves it with the chosen `backend` solver and writes result to `results_db`. +``` + +``` + update_results( + cases_vec::Vector{String}, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) + +Reads `cases_db` to `cases_dict`, accesses the selected cases from `cases_vec`, +solves it with the chosen `backend` solver and writes results to `results_db`. +``` + +``` + update_results( + cases_dict::AbstractDict=upload_cases(json=cases_db); + include_test_tags::Vector{String}=String[], + include_component_tags::Vector{String}=String[], + exclude_test_tags::Vector{String}=String[], + exclude_component_tags::Vector{String}=String[], + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) + +Reads `cases_db` to `cases_dict`, filters the cases according to `include` and `exclude` tags, +solves it with the chosen `backend` solver and writes results to `results_db`. +``` diff --git a/SBMLCases/Project.toml b/SBMLCases/Project.toml deleted file mode 100644 index b628c66dc..000000000 --- a/SBMLCases/Project.toml +++ /dev/null @@ -1,5 +0,0 @@ -[deps] -CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" diff --git a/cases.json b/cases.json index 97b962b34..5c4255db7 100644 --- a/cases.json +++ b/cases.json @@ -1 +1,65633 @@ 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a/cases/output/00025.csv b/cases/output/00025.csv index 3a7da3a96..b8a39440b 100644 --- a/cases/output/00025.csv +++ b/cases/output/00025.csv @@ -1,52 +1,52 @@ time,S1_,S2_ 0.0,0.0015,0.0015 -0.1,0.0013572561270563108,0.0016427438729436892 -0.2,0.0012280961296212644,0.0017719038703787357 -0.3,0.0011112273310284015,0.0018887726689715985 -0.4,0.001005480069060486,0.001994519930939514 -0.5,0.000909795989576898,0.0020902040104231016 -0.6,0.0008232174541496694,0.00217678254585033 -0.7,0.0007448779556962244,0.002255122044303775 -0.8,0.0006739934461852533,0.0023260065538147465 -0.9,0.0006098544896204885,0.0023901455103795114 -1.0,0.0005518191617668046,0.002448180838233195 -1.1,0.0004993066255567155,0.002500693374443284 -1.2,0.0004517913178777756,0.002548208682122224 -1.3,0.0004087976895603041,0.0025912023104396956 -1.4,0.00036989544592145766,0.002630104554078542 -1.5,0.0003346952402314164,0.002665304759768583 -1.6,0.00030284477700044915,0.0026971552229995504 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omitRows: 3 } +include ./table.xlsx type xlsx with { sheet: 3, omitRows: 3 } +include ./table.xlsx type xlsx with { sheet: 4, omitRows: 3 } +// Part 2 +//include ./table1.xlsx type xlsx with { sheet: 1, omitRows: 3 } +//include ./table1.xlsx type xlsx with { sheet: 2, omitRows: 3 } +//include ./table1.xlsx type xlsx with { sheet: 3, omitRows: 3 } +//include ./table1.xlsx type xlsx with { sheet: 4, omitRows: 3 } \ No newline at end of file diff --git a/heta/table.xlsx b/heta/table.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..3f33494bfec1f341866c42810702956053ffb709 GIT binary patch literal 157715 zcmeFad05Tc`#&6tY*7)CG=~fgirO@2P%>16IHDAlsS(X>N)t_zla!L8&JoE}G;9qj zN{I-SElo(X#@%i|_ge4wuAJk1pXa%*=X(D6{>~qt&vm``ey_Fe>2<&E`(8UHo2PIK zaZTmo<>KO!*gcKsTsPYJr57FkFqg+|QApp#O*wgWu6Oj#Btf zjwlsfqs_4HYe~(D?QT<$m2TUhH1e@#`%ax_U(P~yY=JPH0dZ{MeCU{qf;{@){}aFei-UH8=xLE#jSCg| z0y;O21eOlGt&b4U+3c#lFtzU3%A1KypL0VrV4g*#WSGrwF 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"EventWithDelay", + "Parameter" + ], + "testTags": [ + "EventIsPersistent", + "EventT0Firing", + "NonConstantParameter" + ] + } + }, + "01759": { + "name": "01759", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "P1" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolTime", + "EventNoDelay", + "EventWithDelay", + "Parameter" + ], + "testTags": [ + "EventIsPersistent", + "NonConstantParameter" + ] + } + }, + "01760": { + "name": "01760", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "LocalParameters" + ] + } + }, + "01761": { + "name": "01761", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "C", + "avogadro" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount" + ] + } + }, + "01762": { + "name": "01762", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolAvogadro", + "Compartment", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "LocalParameters" + ] + } + }, + "01763": { + "name": "01763", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "C", + "avogadro" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolAvogadro", + "Compartment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount" + ] + } + }, + "01764": { + "name": "01764", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "AssignmentRule", + "Compartment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "InitialValueReassigned", + "LocalParameters", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01765": { + "name": "01765", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Parameter", + "RateRule", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01766": { + "name": "01766", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "InitialAssignment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "InitialValueReassigned", + "LocalParameters", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01767": { + "name": "01767", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "AssignmentRule", + "Compartment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "InitialValueReassigned", + "LocalParameters", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01768": { + "name": "01768", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Parameter", + "RateRule", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01769": { + "name": "01769", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "EventNoDelay", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01770": { + "name": "01770", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "EventNoDelay", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01771": { + "name": "01771", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "EventWithDelay", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01772": { + "name": "01772", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "k0", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "EventNoDelay", + "EventPriority", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonConstantParameter", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01773": { + "name": "01773", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01774": { + "name": "01774", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "S3", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2", + "S3" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "HasOnlySubstanceUnits", + "LocalParameters", + "NonUnityCompartment", + "NonUnityStoichiometry", + "SpeciesReferenceInMath" + ] + } + }, + "01775": { + "name": "01775", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "m_cf", + "s1_cf", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolAvogadro", + "Compartment", + "InitialAssignment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "ConversionFactors", + "InitialValueReassigned" + ] + } + }, + "01776": { + "name": "01776", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "s1_cf", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolAvogadro", + "Compartment", + "InitialAssignment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "ConversionFactors", + "InitialValueReassigned" + ] + } + }, + "01777": { + "name": "01777", + "settings": { + "start": 0.0, + "duration": 10.0, + "steps": 10, + "variables": [ + "S1", + "S2", + "m_cf", + "C" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1", + "S2" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "CSymbolAvogadro", + "Compartment", + "InitialAssignment", + "Parameter", + "Reaction", + "Species" + ], + "testTags": [ + "Amount", + "ConversionFactors", + "InitialValueReassigned" + ] + } + }, + "01778": { + "name": "01778", + "settings": { + "start": 0.0, + "duration": 1.0, + "steps": 10, + "variables": [ + "s1", + "C", + "cf" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "s1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "Compartment", + "Parameter", + "Reaction", + "Species", + "comp:ExternalModelDefinition", + "comp:ReplacedElement", + "comp:SBaseRef", + "comp:Submodel" + ], + "testTags": [ + "Amount", + "comp:ConversionFactor" + ] + } + }, + "01779": { + "name": "01779", + "settings": { + "start": 0.0, + "duration": 1.0, + "steps": 10, + "variables": [ + "C1", + "S1", + "x" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "AssignmentRule", + "CSymbolTime", + "Compartment", + "EventNoDelay", + "Parameter", + "Species" + ], + "testTags": [ + "Amount", + "BoundaryCondition", + "InitialValueReassigned", + "NonConstantCompartment", + "NonConstantParameter", + "NonUnityCompartment" + ] + } + }, + "01780": { + "name": "01780", + "settings": { + "start": 0.0, + "duration": 1.0, + "steps": 10, + "variables": [ + "C1", + "S1", + "x" + ], + "absolute": 0.0001, + "relative": 0.0001, + "amount": [ + "S1" + ], + "concentration": [ + "" + ] + }, + "tags": { + "componentTags": [ + "AssignmentRule", + "CSymbolTime", + "Compartment", + "EventNoDelay", + "Parameter", + "Species" + ], + "testTags": [ + "Amount", + "BoundaryCondition", + "InitialValueReassigned", + "NonConstantCompartment", + "NonConstantParameter", + "NonUnityCompartment" + ] + }, + "result": { + "status": "error", + "message": "Check the model: KeyError(:C1)" + } + } +} diff --git a/src/SBMLCases.jl b/src/SBMLCases.jl index e5e1d1095..cea62e819 100644 --- a/src/SBMLCases.jl +++ b/src/SBMLCases.jl @@ -2,24 +2,60 @@ module SBMLCases using JSON, SimSolver, DataFrames, CSV, DataStructures -const json_path = "./cases.json" -const semantic_path = "./cases/semantic" +# files containing settings and tags of sbml models +const cases_db = "./cases.json" +const results_db = "./results.json" +# models' dirs and output dir paths +const cases_path = "./cases/semantic" const output_path = "./cases/output" +# default backend +const default_backend = Val{:SimSolver} -function add_cases(;cases_path::AbstractString=semantic_path, json_path::AbstractString=json_path) - cases_dict = upload_cases(json=json_path) + +########################## Upload cases from cases_db ######################## + +""" + upload_cases(;json::AbstractString=cases_db) + +Upload cases from `cases_db`. +""" +function upload_cases(;json::AbstractString=cases_db) + f = open(json, "r") + dict = JSON.parse(f, dicttype=OrderedDict) + close(f) + return dict +end + + +########################## Add new cases ##################################### + +""" + add_cases(; + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db + ) + +Add new cases from `cases_path` to `cases_db`. +""" +function add_cases(; + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db +) + cases_dict = upload_cases(json=cases_db) + new_cases = 0 foreach(readdir(cases_path)) do case if !haskey(cases_dict, case) @show case - cases_dict[case] = add_single_case(cases_path, case) + cases_dict[case] = add_single_case(cases_path, case) + new_cases += 1 end end - save_as_json(cases_dict; json=json_path) + new_cases > 0 && save_as_json(cases_dict, cases_db) return nothing end function add_single_case(path::AbstractString, case::AbstractString) - Dict( + OrderedDict( "name" => case, "settings" => add_settings(path, case), "tags" => add_tags(path, case) @@ -28,23 +64,25 @@ end function add_settings(path::AbstractString, case::AbstractString) settings = OrderedDict{String,Any}() - for line in eachline("$path/$case/$case-settings.txt") - split_line = split(line, ":") - - k = first(split_line) - v = last(split_line) - - if k in ["start", "duration", "absolute", "relative"] - settings[k] = !isempty(v) ? parse(Float64, v) : nothing - elseif k == "steps" - settings[k] = !isempty(v) ? parse(Int64, v) : nothing - elseif k in ["variables", "amount", "concentration"] - settings[k] = String[] - for v_i in split(v, ",") - push!(settings[k], strip(v_i)) + open("$path/$case/$case-settings.txt", "r") do f + for line in eachline(f) + split_line = split(line, ":") + + k = first(split_line) + v = last(split_line) + + if k in ["start", "duration", "absolute", "relative"] + settings[k] = !isempty(v) ? parse(Float64, v) : nothing + elseif k == "steps" + settings[k] = !isempty(v) ? parse(Int64, v) : nothing + elseif k in ["variables", "amount", "concentration"] + settings[k] = String[] + for v_i in split(v, ",") + push!(settings[k], strip(v_i)) + end + elseif !isempty(k) + @warn "Case $case: setting $k currently not supported" end - elseif !isempty(k) - @warn "Case $case: setting $k currently not supported" end end return settings @@ -52,47 +90,184 @@ end function add_tags(path::AbstractString, case::AbstractString) tags = OrderedDict{String,Vector{String}}() - flag = 0 - for line in eachline("$path/$case/$case-model.m") - split_line = split(line, ": ") - k = strip(first(split_line)) - v = strip(last(split_line)) - - if k in ["componentTags", "testTags"] - tags[k] = String[] - for v_i in split(v, ",") - push!(tags[k], strip(v_i)) + tags_parsed = 0 + open("$path/$case/$case-model.m", "r") do f + for line in eachline(f) + split_line = split(line, ": ") + k = strip(first(split_line)) + v = strip(last(split_line)) + + if k in ["componentTags", "testTags"] + tags[k] = String[] + for v_i in split(v, ",") + push!(tags[k], strip(v_i)) + end + tags_parsed += 1 end - flag += 1 + tags_parsed == 2 && break end - - flag == 2 && break end return tags end -function save_as_json(dict::AbstractDict; json::AbstractString=json_path) - stringdata = JSON.json(dict) +########################## Save cases or results ############################ + +function save_as_json(dict::AbstractDict, json::AbstractString) + #stringdata = JSON.json(dict) open(json, "w") do f - write(f, stringdata) + JSON.print(f, dict, 4) end return nothing end -function upload_cases(;json::AbstractString=json_path) - f = open(json) - dict = JSON.parse(f, dicttype=OrderedDict) - close(f) - return dict +############# Run simulations and update results in results_db ############## + +""" + update_results( + case::AbstractString, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) + +Reads `cases_db` to `cases_dict`, accesses the `case`, +solves it with the chosen `backend` solver and writes result to `results_db`. +""" +function update_results( + case::AbstractString, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... +) + cases_dict[case]["result"] = OrderedDict() + try + status = solve_case(cases_dict[case], backend; kwargs...) + if status + cases_dict[case]["result"]["status"] = "success" + cases_dict[case]["result"]["message"] = "" + println("$case...................success") + else + cases_dict[case]["result"]["status"] = "failure" + cases_dict[case]["result"]["message"] = "tolerance test not passed" + println("$case...................failure") + end + catch e + cases_dict[case]["result"]["status"] = "error" + cases_dict[case]["result"]["message"] = "Check the model: $e" + println("$case...................error") + finally + save_as_json(cases_dict, results_db) + end + return nothing +end + +""" + update_results( + cases_vec::Vector{String}, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) + +Reads `cases_db` to `cases_dict`, accesses the selected cases from `cases_vec`, +solves it with the chosen `backend` solver and writes results to `results_db`. +""" +function update_results( + cases_vec::Vector{String}, + cases_dict::AbstractDict=upload_cases(json=cases_db); + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... +) + + for case in cases_vec + update_results( + case, + cases_dict; + cases_path=cases_path, + cases_db=cases_db, + results_db=results_db, + backend=default_backend, + kwargs... + ) + end + return nothing end +""" + update_results( + cases_dict::AbstractDict=upload_cases(json=cases_db); + include_test_tags::Vector{String}=String[], + include_component_tags::Vector{String}=String[], + exclude_test_tags::Vector{String}=String[], + exclude_component_tags::Vector{String}=String[], + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... + ) -function solve_case(case::AbstractDict;alg::Symbol=:Vern9) +Reads `cases_db` to `cases_dict`, filters the cases according to `include` and `exclude` tags, +solves it with the chosen `backend` solver and writes results to `results_db`. +""" +function update_results( + cases_dict::AbstractDict=upload_cases(json=cases_db); + include_test_tags::Vector{String}=String[], + include_component_tags::Vector{String}=String[], + exclude_test_tags::Vector{String}=String[], + exclude_component_tags::Vector{String}=String[], + cases_path::AbstractString=cases_path, + cases_db::AbstractString=cases_db, + results_db::AbstractString=results_db, + backend::DataType=default_backend, + kwargs... +) + cases_vec = isempty(include_test_tags) && + isempty(include_component_tags) && + isempty(exclude_test_tags) && + isempty(exclude_component_tags) ? keys(cases_dict) : + filter_cases(cases_dict; + include_test_tags=include_test_tags, + include_component_tags=include_component_tags, + exclude_test_tags=exclude_test_tags, + exclude_component_tags=exclude_component_tags, + ) + update_results( + cases_vec, + cases_dict; + cases_path=cases_path, + cases_db=cases_db, + results_db=results_db, + backend=default_backend, + kwargs... + ) +end + +# solve single model with SimSolver backend +function solve_case( + case::AbstractDict, + backend::Type{Val{:SimSolver}}=default_backend; + cases_path::AbstractString=cases_path, + output_path::AbstractString=output_path, + alg::Symbol=:Vern9 +) case_name = case["name"] - file_path = "$semantic_path/$case_name/julia/model.jl" + file_path = "$cases_path/$case_name/julia/model.jl" isfile(file_path) ? include(file_path) : "julia model for $case_name doesn't exist" - model = eval_model(Main.julia.models) + model = eval_model(SBMLCases.julia.models) tspan = (case["settings"]["start"],case["settings"]["duration"]) step = (case["settings"]["duration"]-case["settings"]["start"])/case["settings"]["steps"] @@ -135,11 +310,13 @@ function solve_case(case::AbstractDict;alg::Symbol=:Vern9) df_sim[!, v] = res[1][ids = v].data end CSV.write("$output_path/$case_name.csv", df_sim) - df_ans = DataFrame!(CSV.File("$semantic_path/$case_name/$case_name-results.csv")) + df_ans = DataFrame!(CSV.File("$cases_path/$case_name/$case_name-results.csv")) return compare_results(case, df_sim, df_ans) end +# tolerance test according to: +# https://github.com/sbmlteam/sbml-test-suite/blob/master/cases/semantic/README.md#tolerances-and-errors-for-timecourse-tests function compare_results(case::AbstractDict, df_sim::DataFrame, df_ans::DataFrame) (i_length,j_length) = size(df_sim) for i in 1:i_length @@ -152,95 +329,18 @@ function compare_results(case::AbstractDict, df_sim::DataFrame, df_ans::DataFram return true end -function update_results( - case::AbstractString; - cases_path::AbstractString=semantic_path, - json_path::AbstractString=json_path, - kwargs... -) - cases_dict = upload_cases(json=json_path) - cases_dict[case]["result"] = OrderedDict() - status = try solve_case(cases_dict[case]; kwargs...) - catch e - cases_dict[case]["result"]["status"] = "error" - cases_dict[case]["result"]["message"] = "Check the model: $e" - save_as_json(cases_dict; json=json_path) - return nothing - end - if status - cases_dict[case]["result"]["status"] = "success" - cases_dict[case]["result"]["message"] = "" - else - cases_dict[case]["result"]["status"] = "failure" - cases_dict[case]["result"]["message"] = "tolerance test not passed" - end - - save_as_json(cases_dict; json=json_path) - return nothing -end - -function update_results( - cases_vec::Vector{String}; - kwargs... -) - cases_dict = upload_cases(json=json_path) - - for case in cases_vec - cases_dict[case]["result"] = OrderedDict() - status = try solve_case(cases_dict[case]; kwargs...) - catch e - cases_dict[case]["result"]["status"] = "error" - cases_dict[case]["result"]["message"] = "Check the model: $e" - continue - end - if status - cases_dict[case]["result"]["status"] = "success" - cases_dict[case]["result"]["message"] = "" - else - cases_dict[case]["result"]["status"] = "failure" - cases_dict[case]["result"]["message"] = "tolerance test not passed" - end - end - save_as_json(cases_dict; json=json_path) - return nothing -end - -function update_results(; - include_test_tags::Vector{String}=String[], - include_component_tags::Vector{String}=String[], - exclude_test_tags::Vector{String}=String[], - exclude_component_tags::Vector{String}=String[], - cases_path::AbstractString=semantic_path, - json_path::AbstractString=json_path, - kwargs... -) - cases_dict = upload_cases(json=json_path) - cases_vec = filter_cases(cases_dict, - include_test_tags, - include_component_tags, - exclude_test_tags, - exclude_component_tags, -) - for case in cases_vec - cases_dict[case]["result"] = OrderedDict() - status = try solve_case(cases_dict[case]; kwargs...) - catch e - cases_dict[case]["result"]["status"] = "error" - cases_dict[case]["result"]["message"] = "Check the model: $e" - continue - end - if status - cases_dict[case]["result"]["status"] = "success" - cases_dict[case]["result"]["message"] = "" - else - cases_dict[case]["result"]["status"] = "failure" - cases_dict[case]["result"]["message"] = "tolerance test not passed" - end - end - save_as_json(cases_dict; json=json_path) - return nothing -end +""" + filter_cases( + cases_dict::AbstractDict; + include_test_tags::Vector{String}=String[], + include_component_tags::Vector{String}=String[], + exclude_test_tags::Vector{String}=String[], + exclude_component_tags::Vector{String}=String[], + ) +Functions replicates the behavior of SBML Runner filter. +It filters out names of the cases which satisfy `include` and `exclude` tags. +""" function filter_cases( cases_dict::AbstractDict; include_test_tags::Vector{String}=String[], @@ -262,6 +362,7 @@ function filter_cases( return filter(x->include_filter_func(x) && exclude_filter_func(x), keys(cases_dict)) end +# update functions after uploading a new model function eval_model(model_code) Model( (cons)->Base.invokelatest(model_code.start, cons), diff --git a/test/runtests.jl b/test/runtests.jl index 0ff0e2992..a811561db 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -2,6 +2,11 @@ using SBMLCases using Test cases_dict = upload_cases() + +@testset "upload test" begin + @test length(cases_dict) == 1780 +end + @testset "filter test" begin s1 = filter_cases( cases_dict,