Fix Raia_CancerResearch2011
Closed this issue · 4 comments
dweindl commented
Importing Raia_CancerResearch2011 fails since Benchmarking-Initiative/Benchmark-Models-PEtab#197
e.g. https://github.com/AMICI-dev/AMICI/actions/runs/7207106512/job/19633280668
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp: In function ‘void amici::model_Raia_CancerResearch2011::sigmay_Raia_CancerResearch2011(amici::realtype*, amici::realtype, const realtype*, const realtype*, const realtype*)’:
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:17:102: error: ‘CD274mRNA’ was not declared in this scope
17 | sigma_observable_CD274mRNA__scaling_CD274mRNA__sd_CD274mRNA_abs_sd_CD274mRNA_rel__model1_data1 = CD274mRNA*noiseParameter2_observable_CD274mRNA__scaling_CD274mRNA__sd_CD274mRNA_abs_sd_CD274mRNA_rel__model1_data1*observableParameter1_observable_CD274mRNA + noiseParameter1_observable_CD274mRNA__scaling_CD274mRNA__sd_CD274mRNA_abs_sd_CD274mRNA_rel__model1_data1; // sigmay[0]
| ^~~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:19:357: error: ‘IL13_DecoyR’ was not declared in this scope
19 | sigma_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 = noiseParameter1_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 + noiseParameter2_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1*observableParameter1_observable_IL13_cell*(IL13_DecoyR + IL13_Rec + p_IL13_Rec + p_IL13_Rec_i); // sigmay[2]
| ^~~~~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:19:371: error: ‘IL13_Rec’ was not declared in this scope
19 | sigma_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 = noiseParameter1_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 + noiseParameter2_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1*observableParameter1_observable_IL13_cell*(IL13_DecoyR + IL13_Rec + p_IL13_Rec + p_IL13_Rec_i); // sigmay[2]
| ^~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:19:382: error: ‘p_IL13_Rec’ was not declared in this scope
19 | sigma_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 = noiseParameter1_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 + noiseParameter2_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1*observableParameter1_observable_IL13_cell*(IL13_DecoyR + IL13_Rec + p_IL13_Rec + p_IL13_Rec_i); // sigmay[2]
| ^~~~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:19:395: error: ‘p_IL13_Rec_i’ was not declared in this scope
19 | sigma_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 = noiseParameter1_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1 + noiseParameter2_observable_IL13_cell__scaling_IL13_cell__sd_IL13_cell_abs_sd_IL13_cell_rel__model1_data1*observableParameter1_observable_IL13_cell*(IL13_DecoyR + IL13_Rec + p_IL13_Rec + p_IL13_Rec_i); // sigmay[2]
| ^~~~~~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:29:102: error: ‘SOCS3mRNA’ was not declared in this scope
29 | sigma_observable_SOCS3mRNA__scaling_SOCS3mRNA__sd_SOCS3mRNA_abs_sd_SOCS3mRNA_rel__model1_data1 = SOCS3mRNA*noiseParameter2_observable_SOCS3mRNA__scaling_SOCS3mRNA__sd_SOCS3mRNA_abs_sd_SOCS3mRNA_rel__model1_data1*observableParameter1_observable_SOCS3mRNA + noiseParameter1_observable_SOCS3mRNA__scaling_SOCS3mRNA__sd_SOCS3mRNA_abs_sd_SOCS3mRNA_rel__model1_data1; // sigmay[12]
| ^~~~~~~~~
/home/runner/work/AMICI/AMICI/test_bmc/Raia_CancerResearch2011/sigmay.cpp:33:304: error: ‘pJAK2’ was not declared in this scope
33 | sigma_observable_pJAK2__scaling_pJAK2__sd_pJAK2_abs_sd_pJAK2_rel__model1_data2 = noiseParameter1_observable_pJAK2__scaling_pJAK2__sd_pJAK2_abs_sd_pJAK2_rel__model1_data2 + noiseParameter2_observable_pJAK2__scaling_pJAK2__sd_pJAK2_abs_sd_pJAK2_rel__model1_data2*observableParameter1_observable_pJAK2*pJAK2; // sigmay[16]
| ^~~~~
Problem in AMICI or in the PEtab problem?
dweindl commented
dweindl commented
Seems like my workaround from #1791 doesn't handle this case properly.
Breaks petab.flatten_timepoint_specific_output_overrides(petab_problem) breaks it.
dweindl commented
Breaks
petab.flatten_timepoint_specific_output_overrides(petab_problem)breaks it.
Bug in libpetab. PEtab-dev/libpetab-python#231 did not adapt petab.flatten_timepoint_specific_output_overrides. observableParameter are not properly replaced in noiseFormula. (-> PEtab-dev/libpetab-python#234)
dweindl commented
Will be fixed in the next libpetab release by PEtab-dev/libpetab-python#235, closing here.