ready to upload

phase-1_2_3/automated_docker_test.sh

@@ -37,8 +37,8 @@ echo "Create submission program"
 cd starting_kit/
 rm -rf submissions
 # Rscript submission_script.R >> logs
-# Rscript submission_script.R 
-python submission_script.py
+Rscript submission_script.R 
+# python submission_script.py
 cd - 
 echo "Done"
 

phase-1_2_3/bundle/FAQ.md

@@ -16,20 +16,20 @@ If your submission fails on Codabench, don't panic, review the logs! You can acc
 
 Try interactive docker or conda environnement, it is especially useful for python user!
 
-A conda environment is provided follow this steps to install and activate it. Retrieve the file [environment-r.yml](https://github.com/bcm-uga/hadaca3/blob/main/docker/codabench_hadaca3_pyr/environment/environment-r.yml) from github as follow:
+A conda environment is provided follow this steps to install and activate it. Retrieve the file [env_final_pyr.yml](https://github.com/bcm-uga/hadaca3/blob/main/docker/codabench_hadaca_final/environment/env_final_pyr.yml) from github as follow:
 
 ``` 
-wget https://raw.githubusercontent.com/bcm-uga/hadaca3/main/docker/codabench_hadaca3_pyr/environment/environment-r.yml
-conda env create -f environment-r.yml && conda activate h3
+wget https://raw.githubusercontent.com/bcm-uga/hadaca3/refs/heads/main/docker/codabench_hadaca_final/environment/env_final_pyr.yml
+conda env create -f env_final_pyr.yml && conda activate h3_final
 ```
 
 To run the docker interactively you can run with: 
 
 ```
 ## for the R version
-sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_pyr R`  and then `source("submission_script.R") 
+sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_final R`  and then `source("submission_script.R") 
 ## for the python version
-sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_pyr python` and then `import submission_script
+sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_final python` and then `import submission_script
 ```
 
 Due to the usage of the super user (sudo) all files created by docker will be owned by root. In order to retrieve ownership, you can use this command:

phase-1_2_3/bundle/submission.md

@@ -73,16 +73,16 @@ Then follow steps 4 and 5 described above.
 
 ```
 cd starting_kit
-sudo docker pull hombergn/hadaca3_pyr
-sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_pyr R
+sudo docker pull hombergn/hadaca3_final
+sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_final R
 source("submission_script.R")
 chown -R $USER submissions #if necessary
 ```
 
 Alternatively, run the following commande to execute the `submission_script`:
 
 ```
-sudo docker run -v .:/hadaca3 -w /hadaca3  hombergn/hadaca3_pyr Rscript submission_script.R
+sudo docker run -v .:/hadaca3 -w /hadaca3  hombergn/hadaca3_final Rscript submission_script.R
 ```
 
 and regain ownership of the files generated with:

phase-1_2_3/generate_bundle.sh

@@ -30,22 +30,23 @@ mkdir starting_kit
 #  generate baselines :
 rm -rf ~/projects/hadaca3/templates/tmp/
 Rscript ~/projects/hadaca3/templates/generate_baselines.R Phase_1  
-cp ~/projects/hadaca3/templates/tmp/* starting_kit/
+cp -R ~/projects/hadaca3/templates/tmp/* starting_kit/
 
 
 # rm -rf starting_kit_phase1
 mkdir starting_kit_phase1
 
 rm -rf ~/projects/hadaca3/templates/tmp/
 Rscript ~/projects/hadaca3/templates/generate_baselines.R Phase_1_only  
-cp ~/projects/hadaca3/templates/tmp/* starting_kit_phase1/
+cp -R ~/projects/hadaca3/templates/tmp/* starting_kit_phase1/
 
 rm -r ~/projects/hadaca3/templates/tmp/ 
 
 
 #### Put input data inside the bundle ! 
-cd starting_kit/ ; zip  -FS  -r  ../bundle/starting_kit_phase2-3.zip *  -x \*submissions\* ; cd .. ; 
-cd starting_kit_phase1/ ; zip  -FS  -r  ../bundle/starting_kit_phase1.zip *  -x \*submissions\* ; cd .. ; 
+# cd starting_kit/ ; zip  -FS  -r  ../bundle/starting_kit_phase2-3.zip *  -x \*submissions\* ; cd .. ; 
+# cd starting_kit_phase1/ ; zip  -FS  -r  ../bundle/starting_kit_phase1.zip *  -x \*submissions\* ; cd .. ; 
+
 zip -FS -r -j bundle/input_data_phase2.zip input_data/
 zip -FS -r -j bundle/input_data_phase3.zip input_data_final/
 zip -FS -r -j bundle/input_data_phase1.zip input_data_phase1/
@@ -67,15 +68,15 @@ zip -FS -j -r  bundle/ground_truth_phase1.zip ground_truth_phase1/
 
 
 # ##### generate starting_kit and input_data outisde bundle.zip
-# cd starting_kit_phase1/ ; zip  -FS  -r  ../bundle/starting_kit_phase1.zip *  -x \*submissions\* -x \*data\* ; cd .. ; 
-# cd starting_kit/ ; zip  -FS  -r  ../bundle/starting_kit_phase2-3.zip *  -x \*submissions\* -x \*data\* ; cd .. ; 
+cd starting_kit_phase1/ ; zip  -FS  -r  ../bundle/starting_kit_phase1.zip *  -x \*submissions\* -x \*data\* ; cd .. ; 
+cd starting_kit/ ; zip  -FS  -r  ../bundle/starting_kit_phase2-3.zip *  -x \*submissions\* -x \*data\* ; cd .. ; 
 
-# zip -FS -r -j input_data_phase2.zip input_data/
-# zip -FS -r -j input_data_phase3.zip input_data_final/
-# zip -FS -r -j input_data_phase1.zip input_data_phase1/
+zip -FS -r -j input_data_phase2.zip input_data/
+zip -FS -r -j input_data_phase3.zip input_data_final/
+zip -FS -r -j input_data_phase1.zip input_data_phase1/
 
-# cd starting_kit/ ; zip  -FS  -r  ../starting_kit_phase2-3.zip *  -x \*submissions\* ; cd .. ; 
-# cd starting_kit_phase1/ ; zip  -FS  -r  ../starting_kit_phase1.zip *  -x \*submissions\* ; cd .. ; 
+cd starting_kit/ ; zip  -FS  -r  ../starting_kit_phase2-3.zip *  -x \*submissions\* ; cd .. ; 
+cd starting_kit_phase1/ ; zip  -FS  -r  ../starting_kit_phase1.zip *  -x \*submissions\* ; cd .. ; 
 
 
 

phase-1_2_3/generate_data.sh

@@ -98,6 +98,8 @@ do
 done
 
 
+# rm -rf starting_kit
+# rm -rf starting_kit_phase1
 
 
 mkdir starting_kit/data/

phase-1_2_3/ingestion_program/sub_ingestion.py

@@ -21,11 +21,9 @@
 try:
     # Define the target and link name
     target = "../ingested_program/attachement/"
-    link_name = "attachement/"
+    link_name = "attachement"
 
-    # Create a symbolic link
     os.symlink(target, link_name)
-    # print(f"Symbolic link created: {link_name} -> {target}")
 except FileExistsError:
     # Handle the case where the symbolic link already exists
     os.unlink(link_name)  # Remove the existing symbolic link

phase-1_2_3/scoring_program/detailed_results.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Visualize Results"
-author: "Elise Amblard, Hugo Barbot, Florent Chuffart and Magali Richard"
+# author: "Elise Amblard, Hugo Barbot, Florent Chuffart and Magali Richard"
 date: "`r Sys.Date()`"
 output: 
   # prettydoc::html_pretty: # create a styles.css file and snakemake doesn't like it

phase-1_2_3/scoring_program/scoring.R

@@ -226,7 +226,7 @@ scoring_function <- function(A_real, A_pred) {
   else if (nrow(A_pred) > nrow(A_real) & setequal(rownames(A_real), c("basal",'classic'))) { # partial ground truth only for the in vivo dataset
     rmse = NA
     mae = NA
-    aitchison = eval_Aitchison(A_real, A_pred[rownames(A_real),])
+    aitchison = NA
     pearson_tot = NA
     pearson_col = NA
     pearson_row = correlationP_row(A_real, A_pred[rownames(A_real),])
@@ -277,6 +277,11 @@ scoring_function <- function(A_real, A_pred) {
   }
   judge_candidate_norm = apply(judge_candidate, 2, CenterScaleNorm)
 
+  # transform scores s.t. 1 is the best score
+  judge_candidate_norm = 1 - judge_candidate_norm
+  judge_candidate_norm[,grep("pearson",colnames(judge_candidate_norm))] = 1 - judge_candidate_norm[,grep("pearson",colnames(judge_candidate_norm))]
+  judge_candidate_norm[,grep("spearman",colnames(judge_candidate_norm))] = 1 - judge_candidate_norm[,grep("spearman",colnames(judge_candidate_norm))]
+
   # Average over judges with the geometric mean for the candidate of interest
   #score_aggreg = exp(mean(log(judge_candidate_norm[1,]),na.rm=T))
   weights = c(1/3*1/2,1/3*1/2,