diff --git a/.github/workflows/build-and-simulate.yml b/.github/workflows/build-and-simulate.yml index 918c103fa..a51c9c619 100644 --- a/.github/workflows/build-and-simulate.yml +++ b/.github/workflows/build-and-simulate.yml @@ -19,10 +19,11 @@ jobs: platform: [ ubuntu-latest ] runs-on: [self-hosted,Julia] # ${{ matrix.platform }} - + timeout-minutes: 1440 defaults: run: shell: bash + steps: - name: Checkout uses: actions/checkout@v2 @@ -38,7 +39,6 @@ jobs: npm i -g https://github.com/insysbio/heta-compiler.git - run: | heta build - heta_version=`heta -v` #- name: Setup Julia environment (disabled for self-hosted server) # uses: julia-actions/setup-julia@v1.1.12 # with: @@ -48,7 +48,7 @@ jobs: - name: SimSolver installation run: julia -e 'using Pkg;Pkg.activate(".");Pkg.add(url="https://${{ secrets.SIMSOLVER_GITLAB_TOKEN }}@gitlab.insysbio.com/dev-group/simsolver", rev="dev");Pkg.build()' - name: Run Julia simulations - run: julia ./run.jl $heta_version + run: julia ./run.jl `heta -v` - name: Copy files to "static" run: | mkdir -p ./result/cases/output diff --git a/.github/workflows/copy-visualization.yml b/.github/workflows/copy-visualization.yml index 0f10a333a..827c73873 100644 --- a/.github/workflows/copy-visualization.yml +++ b/.github/workflows/copy-visualization.yml @@ -21,11 +21,11 @@ jobs: uses: actions/checkout@v2 with: persist-credentials: false - - name: Copy results (TEMPORAL) - run: | - mkdir -p ./static/cases/output - cp -rf ./cases/output/*.png ./static/cases/output/ | true - cp -f ./results.json ./static/ | true + #- name: Copy results (TEMPORAL) + # run: | + # mkdir -p ./static/cases/output + # cp -rf ./cases/output/*.png ./static/cases/output/ | true + # cp -f ./results.json ./static/ | true - name: Deploy to "result" branch only for "master" and "*-result" pushes uses: JamesIves/github-pages-deploy-action@releases/v3 with: diff --git a/.gitignore b/.gitignore index 957deba73..cf852721a 100644 --- a/.gitignore +++ b/.gitignore @@ -3,9 +3,9 @@ /cases/semantic/*/output.json /cases/semantic/*/julia /cases/output/*.csv -#/cases/output/*.png +/cases/output/*.png /build.log -#/results.json +/results.json /cases/semantic/julia /cases/semantic/json.json diff --git a/results.json b/results.json deleted file mode 100644 index 5aec16fa0..000000000 --- a/results.json +++ /dev/null @@ -1,66899 +0,0 @@ -{ - 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] - } - }, - "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" - ] - } - } - }, - "heta_version": "0.5.12" -} diff --git a/run.jl b/run.jl index 92921c232..f79397cef 100644 --- a/run.jl +++ b/run.jl @@ -10,30 +10,11 @@ build_dict = JSON.parsefile("./build.log"; dicttype = OrderedDict) ### run all cases -required_time = @elapsed begin - for (id, value) in collect(cases_dict)[1:150] - build_errors = case_build_errors( - value; - build_dict = build_dict - ) - value["build_errors"] = build_errors - - if (length(build_errors) == 0) - sim_report = case_sim_result( - value; - cases_path = "./cases/semantic", - output_path = "./cases/output" - ) - else - sim_report = Dict( - "status" => "SKIPPED", - "message" => "Model was not simulated because of build errors" - ) - end - - value["result"] = sim_report - end -end +required_time = @elapsed run_and_update_status!( + cases_dict; + build_dict = build_dict, + range = 1:1780 +) #heta_version = ENV["heta_version"] date = Dates.format(Dates.now(), "yyyy-mm-dd HH:MM:SS") diff --git a/src/SBMLCases.jl b/src/SBMLCases.jl index 7a97dd8ee..138b58361 100644 --- a/src/SBMLCases.jl +++ b/src/SBMLCases.jl @@ -2,7 +2,6 @@ module SBMLCases using JSON, SimSolver, DataFrames, CSV, DataStructures, StatsPlots - # files containing settings and tags of sbml models const cases_db = "./cases.json" const results_db = "./results.json" @@ -532,7 +531,38 @@ function plot_results(df_sim, df_ans) plot(p_sim, p_ans, p_diff, legend, dpi=300) end +### ### +function run_and_update_status!( + cases_dict::OrderedDict; + build_dict::Vector{Any} = OrderedDict(), + range::UnitRange{Int64} = 1:1780 +) + for (id, value) in collect(cases_dict)[range] + build_errors = case_build_errors( + value; + build_dict = build_dict + ) + value["build_errors"] = build_errors + + if (length(build_errors) == 0) + sim_report = case_sim_result( + value; + cases_path = "./cases/semantic", + output_path = "./cases/output" + ) + else + sim_report = Dict( + "status" => "SKIPPED", + "message" => "Model was not simulated because of build errors" + ) + end + + value["result"] = sim_report + end +end +### ### + export upload_cases, filter_cases, add_cases, update_results, - case_build_errors, case_sim_result # Metelkin + case_build_errors, case_sim_result, run_and_update_status! # Metelkin end #module