Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix Raia_CancerResearch2011 #2238

Closed
dweindl opened this issue Dec 14, 2023 · 4 comments
Closed

Fix Raia_CancerResearch2011 #2238

dweindl opened this issue Dec 14, 2023 · 4 comments
Assignees
@dweindl
Labels
PEtab PEtab-import related

Comments

@dweindl
Copy link
Member

dweindl commented Dec 14, 2023

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 dweindl added the PEtab PEtab-import related label Dec 14, 2023
@dweindl
Copy link
Member Author

dweindl commented Dec 14, 2023

See also #609 #919

Seems like my workaround from #1791 doesn't handle this case properly.

@dweindl dweindl self-assigned this Dec 14, 2023
@dweindl
Copy link
Member Author

dweindl commented Dec 14, 2023

Seems like my workaround from #1791 doesn't handle this case properly.

Breaks petab.flatten_timepoint_specific_output_overrides(petab_problem) breaks it.

@dweindl
Copy link
Member Author

dweindl commented Dec 14, 2023 •
edited
Loading

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
Copy link
Member Author

dweindl commented Dec 14, 2023

Will be fixed in the next libpetab release by PEtab-dev/libpetab-python#235, closing here.

@dweindl dweindl closed this as completed Dec 14, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@dweindl dweindl

Labels
PEtab PEtab-import related
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@dweindl