run_sythea is constantly rebuilding the app

[amalic]

I expected the build only to run once. But when running run_synthea, packages are being downloaded and the some build is running.

Would be great if run_synthea would just start the prebuilt app!

[jawalonoski]

That shouldn't be happening. Please try ./gradlew run --console=verbose and post the results here.

[RJBeetel3]

having the same problem. I ran the above and got the output below `

Task :versionTxt Task :compileJava UP-TO-DATE Task :processResources UP-TO-DATE Task :classes UP-TO-DATE

Task :run Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dementia.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/colorectal_cancer.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/self_harm.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/osteoporosis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_substance_abuse_conditions.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_substance_abuse_treatment.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/epilepsy.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/mTBI.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/primary_atrophic_hypothyroidism.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/attention_deficit_disorder.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/medications/ear_infection_antibiotic.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/medications/moderate_opioid_pain_reliever.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/medications/strong_opioid_pain_reliever.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/medications/otc_pain_reliever.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/medications/otc_antihistamine.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/gallstones.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/sore_throat.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/homelessness.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/congestive_heart_failure.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/total_joint_replacement/functional_status_assessments.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/lung_cancer.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/sexual_activity.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/appendicitis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_lung_cancer.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/opioid_addiction.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/osteoarthritis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/pregnancy.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/female_sterilization.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/patch_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/oral_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/injectable_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/implant_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/ring_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/male_sterilization.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/clear_contraceptive.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptives/intrauterine_device.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/surgery/general_anesthesia.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/contraceptive_maintenance.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_self_harm.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/fibromyalgia.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_hyperlipidemia.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/lupus.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/cystic_fibrosis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dialysis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/rheumatoid_arthritis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/urinary_tract_infections.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/metabolic_syndrome_care.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/bronchitis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/asthma.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/sinusitis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/copd.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/gout.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/injuries.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_prostate_cancer.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/wellness_encounters.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/lung_cancer/lung_cancer_probabilities.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/food_allergies.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_ptsd.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/atopy.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/hypothyroidism.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/outgrow_env_allergies.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/allergy_panel.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/outgrow_food_allergies.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/severe_allergic_reaction.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/allergy_incidence.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergies/immunotherapy.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/allergic_rhinitis.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/female_reproduction.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veteran_mdd.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/early_severe_eczema_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/moderate_cd_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/severe_cd_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/early_moderate_eczema_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/mid_moderate_eczema_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/dermatitis/mid_severe_eczema_obs.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/veterans/veteran_suicide_probabilities.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/med_rec.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/metabolic_syndrome_disease.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/ear_infections.json Loading /Users/robertbeetel/Workspace/synthea/build/resources/main/modules/total_joint_replacement.json Loaded 88 modules. Running with options: Population: 1 Seed: 1540426208921 Location: Massachusetts Min Age: 0 Max Age: 140 1 -- Antonio44 Koch169 (44 y/o M) Milton, Massachusetts {alive=1, dead=0}`

[jawalonoski]

When it says UP-TO-DATE it is not actually compiling anything... it checks that no changes have been made since it was last compiled, and if there weren't, it says UP-TO-DATE and moves on it's merry way.

If it was recompiling, you'd see something like this instead:

Starting a Gradle Daemon (subsequent builds will be faster)
> Task :versionTxt

> Task :compileJava
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :processResources
> Task :classes

> Task :run
Loading /Users/jwalonoski/git/synthea/build/resources/main/modules/dementia.json
Loading /Users/jwalonoski/git/synthea/build/resources/main/modules/colorectal_cancer.json
Loading /Users/jwalonoski/git/synthea/build/resources/main/modules/self_harm.json
Loading /Users/jwalonoski/git/synthea/build/resources/main/modules/osteoporosis.json
...

[jawalonoski]

I can't replicate this issue. Can someone provide steps to reproduce and logs that verify this? If not, I'm going to close this issue.

[jawalonoski]

For clarity, when it says something like

Loading /path/synthea/build/resources/main/modules/dementia.json

These files are not being compiled or downloaded, they are simply being loaded from the local file system into the program memory for execution.

[amalic]

I have created a Dockerfile (plz let me know if you want me to do a pull request). Because gradlew was not working properly I used gradle directly. You will also notice that I removed automated Testing and recompilation when running the command.

To run it you will need Docker on you machine.

Build

docker build --rm -t synthea .

Run You can add your command line arguments after below command. Those will be passed to the command executed in the ENTRYPOINT directive of Docker.

docker run -i --rm -v <local_dir>:/data synthea

Update: Feel free to play around and replace gradle again with gradlew. You'll notice that both build and running the app will take longer via gradlew.

[amalic]

For clarity, when it says something like

Loading /path/synthea/build/resources/main/modules/dementia.json

These files are not being compiled or downloaded, they are simply being loaded from the local file system into the program memory for execution.

Can't you package it in a FAT jar instead and run it via java -jar <fatjar>

[jawalonoski]

Sure, we could package them in a jar... However, the idea was that some people will add, modify, or delete JSON modules after compilation. One long-term goal was that you could use the Module Builder to make such model changes, and then hit a "run" or "execute" button -- which would drop the changes into the modules folder and then generate some patients dynamically.

Regarding docker... I have no strong feelings about this. To be honest, I'm a docker newbie. What sort of maintenance would be required by the project?