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updated API (results file, backend, etc), documentation, tests
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| # SBMLCases | ||
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| 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. | ||
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| ## Overview | ||
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| 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/<case_num>/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`). | ||
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| Currently SBMLCases.jl suport only one `SimSolver` Simulation Backend. | ||
|
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| ## Usage | ||
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| SBMLCases.jl exports the following functions: | ||
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| ``` | ||
| upload_cases(;json::AbstractString=cases_db) | ||
| Upload cases from `cases_db`. | ||
| ``` | ||
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| ``` | ||
| add_cases(; | ||
| cases_path::AbstractString=cases_path, | ||
| cases_db::AbstractString=cases_db | ||
| ) | ||
| Add new cases from `cases_path` to `cases_db`. | ||
| ``` | ||
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| ``` | ||
| 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`. | ||
| ``` | ||
|
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| ``` | ||
| 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`. | ||
| ``` | ||
|
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| ``` | ||
| 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`. | ||
| ``` |
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| @@ -1,52 +1,52 @@ | ||
| time,S1,S2 | ||
| 0.0,0.15,0.0 | ||
| 0.2,0.14297458165320048,0.01405083669359902 | ||
| 0.4,0.1418174316918867,0.016365136616226572 | ||
| 0.6,0.14171058305413248,0.016578833891735045 | ||
| 0.8,0.14170134081015617,0.01659731837968766 | ||
| 1.0,0.14170054618455744,0.01659890763088515 | ||
| 1.2,0.14170047790024573,0.016599044199508535 | ||
| 1.4,0.14170047203265482,0.016599055934690368 | ||
| 1.6,0.14170047152846155,0.016599056943076902 | ||
| 1.8,0.14170047148513698,0.016599057029725996 | ||
| 2.0,0.14170047148141418,0.01659905703717163 | ||
| 2.2,0.1417004714810943,0.016599057037811425 | ||
| 2.4,0.1417004714810668,0.01659905703786641 | ||
| 2.6,0.14170047148106443,0.016599057037871123 | ||
| 2.8,0.14170047148106424,0.016599057037871533 | ||
| 3.0,0.1417004714810642,0.01659905703787156 | ||
| 3.2,0.1417004714810642,0.01659905703787157 | ||
| 3.4,0.1417004714810642,0.01659905703787157 | ||
| 3.6,0.1417004714810642,0.01659905703787156 | ||
| 3.8,0.1417004714810642,0.01659905703787157 | ||
| 4.0,0.1417004714810642,0.01659905703787157 | ||
| 4.2,0.1417004714810642,0.01659905703787156 | ||
| 4.4,0.1417004714810642,0.01659905703787157 | ||
| 4.6,0.1417004714810642,0.01659905703787157 | ||
| 4.8,0.1417004714810642,0.01659905703787156 | ||
| 5.0,0.1417004714810642,0.01659905703787157 | ||
| 5.2,0.1417004714810642,0.01659905703787157 | ||
| 5.4,0.1417004714810642,0.01659905703787156 | ||
| 5.6,0.1417004714810642,0.01659905703787157 | ||
| 5.8,0.1417004714810642,0.01659905703787157 | ||
| 6.0,0.1417004714810642,0.01659905703787156 | ||
| 6.2,0.1417004714810642,0.01659905703787157 | ||
| 6.4,0.1417004714810642,0.01659905703787157 | ||
| 6.6,0.1417004714810642,0.01659905703787156 | ||
| 6.8,0.1417004714810642,0.01659905703787157 | ||
| 7.0,0.1417004714810642,0.01659905703787157 | ||
| 7.2,0.1417004714810642,0.01659905703787156 | ||
| 7.4,0.1417004714810642,0.01659905703787157 | ||
| 7.6,0.1417004714810642,0.01659905703787157 | ||
| 7.8,0.1417004714810642,0.01659905703787156 | ||
| 8.0,0.1417004714810642,0.01659905703787157 | ||
| 8.2,0.1417004714810642,0.01659905703787157 | ||
| 8.4,0.1417004714810642,0.01659905703787156 | ||
| 8.6,0.1417004714810642,0.01659905703787157 | ||
| 8.8,0.1417004714810642,0.01659905703787157 | ||
| 9.0,0.1417004714810642,0.01659905703787156 | ||
| 9.2,0.1417004714810642,0.01659905703787157 | ||
| 9.4,0.1417004714810642,0.01659905703787157 | ||
| 9.6,0.1417004714810642,0.01659905703787156 | ||
| 9.8,0.1417004714810642,0.01659905703787157 | ||
| 10.0,0.1417004714810642,0.016599057037871567 | ||
| time,S1_,S2_ | ||
| 0.0,1.0,0.0 | ||
| 0.2,0.8187307530780784,0.18126924692192162 | ||
| 0.4,0.670320046061308,0.329679953938692 | ||
| 0.6,0.5488116361228628,0.4511883638771372 | ||
| 0.8,0.4493289641373483,0.5506710358626518 | ||
| 1.0,0.3678794411471917,0.6321205588528083 | ||
| 1.2,0.3011942131376173,0.6988057868623827 | ||
| 1.4,0.2465969648338056,0.7534030351661943 | ||
| 1.6,0.2018965184687337,0.7981034815312663 | ||
| 1.8,0.16529888784824678,0.8347011121517531 | ||
| 2.0,0.1353352826311758,0.8646647173688241 | ||
| 2.2,0.11080315786667538,0.8891968421333246 | ||
| 2.4,0.9071795440746309,0.992820455925369 | ||
| 2.6,0.7427357988087016,1.1572642011912984 | ||
| 2.8,0.6081006435600884,1.2918993564399115 | ||
| 3.0,0.49787069229346204,1.402129307706538 | ||
| 3.2,0.40762204704550836,1.4923779529544916 | ||
| 3.4,0.333732697460766,1.566267302539234 | ||
| 3.6,0.27323722298126396,1.6267627770187358 | ||
| 3.8,0.2237077218051885,1.6762922781948113 | ||
| 4.0,0.18315639109018358,1.7168436089098162 | ||
| 4.2,0.14995576812061612,1.7500442318793836 | ||
| 4.4,0.12277339850590555,1.7772266014940943 | ||
| 4.6,0.10051835367024856,1.7994816463297512 | ||
| 4.8,0.8229746743641412,1.9770253256357582 | ||
| 5.0,0.6737946895232741,2.126205310476625 | ||
| 5.2,0.5516564298513958,2.2483435701485033 | ||
| 5.4,0.45165807935100505,2.348341920648894 | ||
| 5.6,0.3697863566445127,2.4302136433553865 | ||
| 5.8,0.3027554524245839,2.4972445475753156 | ||
| 6.0,0.24787520029794746,2.552124799701952 | ||
| 6.2,0.20294305204381505,2.5970569479560845 | ||
| 6.4,0.16615571645640692,2.6338442835434925 | ||
| 6.6,0.13603679465494573,2.663963205344954 | ||
| 6.8,0.11137750558685111,2.6886224944130483 | ||
| 7.0,0.9118818751654232,2.7881181248344564 | ||
| 7.2,0.7465857487503395,2.95341425124954 | ||
| 7.4,0.6112527298431759,3.0887472701567034 | ||
| 7.6,0.5004513941647138,3.1995486058351656 | ||
| 7.8,0.40973494346376443,3.290265056536115 | ||
| 8.0,0.3354625898996394,3.36453741010024 | ||
| 8.2,0.27465352496216977,3.4253464750377094 | ||
| 8.4,0.22486728784005916,3.47513271215982 | ||
| 8.6,0.18410576488189817,3.515894235117981 | ||
| 8.8,0.15073305079560467,3.5492669492042745 | ||
| 9.0,0.12340978423008243,3.5765902157697966 | ||
| 9.2,0.10103938457103766,3.5989606154288416 | ||
| 9.4,0.8272405340680946,3.7727594659317623 | ||
| 9.6,0.6772872655599373,3.9227127344399193 | ||
| 9.8,0.5545159129551971,4.04548408704466 | ||
| 10.0,0.4539992307842085,4.146000769215648 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,52 +1,52 @@ | ||
| time,S1,S2 | ||
| time,S1_,S2_ | ||
| 0.0,0.00015,0.00015 | ||
| 0.1,0.00013572561271483168,0.0001642743872851683 | ||
| 0.2,0.00012280961297877655,0.00017719038702122342 | ||
| 0.3,0.00011112273312543865,0.00018887726687456132 | ||
| 0.4,0.00010054800693331254,0.00019945199306668743 | ||
| 0.5,9.09795989885266e-5,0.00020902040101147338 | ||
| 0.6,8.23217454484497e-5,0.0002176782545515503 | ||
| 0.7,7.44877956049683e-5,0.0002255122043950317 | ||
| 0.8,6.739934465507645e-5,0.00023260065534492353 | ||
| 0.9,6.098544899925579e-5,0.0002390145510007442 | ||
| 1.0,5.518191621408741e-5,0.00024481808378591256 | ||
| 1.1,4.993066259290346e-5,0.0002500693374070965 | ||
| 1.2,4.517913182452901e-5,0.00025482086817547097 | ||
| 1.3,4.087976899205568e-5,0.00025912023100794427 | ||
| 1.4,3.698954462725026e-5,0.0002630104553727497 | ||
| 1.5,3.346952405717435e-5,0.0002665304759428256 | ||
| 1.6,3.0284477732891922e-5,0.000269715522267108 | ||
| 1.7,2.7402528640302895e-5,0.000272597471359697 | ||
| 1.8,2.479483326427223e-5,0.00027520516673572765 | ||
| 1.9,2.2435292913036245e-5,0.0002775647070869636 | ||
| 2.0,2.0300292513723772e-5,0.0002796997074862761 | ||
| 2.1,1.8368464264769808e-5,0.00028163153573523006 | ||
| 2.2,1.6620473779775818e-5,0.000283379526220224 | ||
| 2.3,1.5038826582472454e-5,0.00028496117341752743 | ||
| 2.4,1.3607693016121149e-5,0.0002863923069838787 | ||
| 2.5,1.2312749814989193e-5,0.0002876872501850107 | ||
| 2.6,1.1141036752292259e-5,0.0002888589632477076 | ||
| 2.7,1.0080826929888836e-5,0.00028991917307011106 | ||
| 2.8,9.121509411542257e-6,0.0002908784905884576 | ||
| 2.9,8.253483025104512e-6,0.0002917465169748954 | ||
| 3.0,7.468060270758482e-6,0.0002925319397292414 | ||
| 3.1,6.757380373599913e-6,0.0002932426196264 | ||
| 3.2,6.114330610360177e-6,0.0002938856693896397 | ||
| 3.3,5.532475122881242e-6,0.00029446752487711863 | ||
| 3.4,5.005990505884135e-6,0.0002949940094941157 | ||
| 3.5,4.529607524371697e-6,0.00029547039247562816 | ||
| 3.6,4.098558377353737e-6,0.00029590144162264617 | ||
| 3.7,3.7085289800922824e-6,0.0002962914710199076 | ||
| 3.8,3.355615787291567e-6,0.0002966443842127083 | ||
| 3.9,3.036286725104735e-6,0.00029696371327489517 | ||
| 4.0,2.7473458409516654e-6,0.00029725265415904824 | ||
| 4.1,2.4859013173513956e-6,0.0002975140986826485 | ||
| 4.2,2.2493365296408347e-6,0.00029775066347035906 | ||
| 4.3,2.0352838579157028e-6,0.0002979647161420842 | ||
| 4.4,1.8416009910947652e-6,0.0002981583990089051 | ||
| 4.5,1.6663494859505222e-6,0.00029833365051404933 | ||
| 4.6,1.507775366517863e-6,0.000298492224633482 | ||
| 4.7,1.3642915697131113e-6,0.0002986357084302867 | ||
| 4.8,1.234462061473277e-6,0.00029876553793852656 | ||
| 4.9,1.1169874644444974e-6,0.00029888301253555533 | ||
| 5.0,1.010692053376773e-6,0.00029898930794662306 | ||
| 0.1,0.00013572561270539372,0.00016427438729460625 | ||
| 0.2,0.00012280961296169915,0.00017719038703830083 | ||
| 0.3,0.00011112273310186594,0.00018887726689813402 | ||
| 0.4,0.00010054800690935297,0.000199451993090647 | ||
| 0.5,9.097959900104418e-5,0.00020902040099895578 | ||
| 0.6,8.232174548052376e-5,0.0002176782545194762 | ||
| 0.7,7.448779561149164e-5,0.00022551220438850832 | ||
| 0.8,6.739934464387997e-5,0.00023260065535611997 | ||
| 0.9,6.0985448993379165e-5,0.0002390145510066208 | ||
| 1.0,5.518191618163733e-5,0.0002448180838183626 | ||
| 1.1,4.993066253462524e-5,0.0002500693374653747 | ||
| 1.2,4.517913175659991e-5,0.00025482086824340003 | ||
| 1.3,4.087976904930237e-5,0.0002591202309506976 | ||
| 1.4,3.69895450294831e-5,0.0002630104549705168 | ||
| 1.5,3.346952473523824e-5,0.0002665304752647617 | ||
| 1.6,3.0284478365190325e-5,0.00026971552163480964 | ||
| 1.7,2.7402528989385644e-5,0.0002725974710106143 | ||
| 1.8,2.47948333884863e-5,0.00027520516661151364 | ||
| 1.9,2.243529302392129e-5,0.00027756470697607865 | ||
| 2.0,2.0300292641689512e-5,0.00027969970735831044 | ||
| 2.1,1.8368464166747164e-5,0.0002816315358332528 | ||
| 2.2,1.662047335351365e-5,0.0002833795266464863 | ||
| 2.3,1.5038826133057045e-5,0.0002849611738669429 | ||
| 2.4,1.360769260798726e-5,0.00028639230739201273 | ||
| 2.5,1.2312749569337599e-5,0.0002876872504306624 | ||
| 2.6,1.1141036811850394e-5,0.0002888589631881496 | ||
| 2.7,1.0080827264386651e-5,0.00028991917273561333 | ||
| 2.8,9.121509816299667e-6,0.0002908784901837003 | ||
| 2.9,8.253483279589298e-6,0.00029174651672041066 | ||
| 3.0,7.4680602981646e-6,0.00029253193970183534 | ||
| 3.1,6.757380269461924e-6,0.00029324261973053803 | ||
| 3.2,6.114330518983007e-6,0.000293885669481017 | ||
| 3.3,5.532475064993293e-6,0.0002944675249350067 | ||
| 3.4,5.00599032869343e-6,0.00029499400967130654 | ||
| 3.5,4.529607084618693e-6,0.00029547039291538126 | ||
| 3.6,4.098557806808657e-6,0.0002959014421931913 | ||
| 3.7,3.7085284580834826e-6,0.0002962914715419165 | ||
| 3.8,3.35561532243618e-6,0.00029664438467756377 | ||
| 3.9,3.036286354594513e-6,0.00029696371364540543 | ||
| 4.0,2.7473455857585875e-6,0.0002972526544142414 | ||
| 4.1,2.4859011472762736e-6,0.0002975140988527237 | ||
| 4.2,2.2493363815390695e-6,0.0002977506636184609 | ||
| 4.3,2.03528368149191e-6,0.00029796471631850804 | ||
| 4.4,1.8416007808291556e-6,0.0002981583992191708 | ||
| 4.5,1.6663492739613116e-6,0.00029833365072603866 | ||
| 4.6,1.5077751822807639e-6,0.0002984922248177192 | ||
| 4.7,1.3642914011327701e-6,0.0002986357085988672 | ||
| 4.8,1.2344618601896144e-6,0.00029876553813981037 | ||
| 4.9,1.116987208676993e-6,0.00029888301279132296 | ||
| 5.0,1.010691796069831e-6,0.00029898930820393014 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,4 @@ | ||
| time,S1,S2 | ||
| time,S1_,S2_ | ||
| 0.0,0.0015,0.0015 | ||
| 0.1,0.0015,0.0015 | ||
| 0.2,0.0015,0.0015 | ||
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