Advanced Disease Rework (#28451)

* Reworks cures, adds strains, adds treatment chems to symptoms

* Enables coexistence of different samples of the same strain at different stages within the same container

* Adds symptom guessing. Correct guesses reduce analysis time and wrong ones increase it.

* Adds a chance for a virus to evolve into a new strain. changing the cure and adding/subtracting symptoms

* Revert "Adds a chance for a virus to evolve into a new strain. changing the cure and adding/subtracting symptoms"

This reverts commit 124dd485c7.

* Adds spontaneous virus mutations, strain tracking. Removes antibody metabolism

* change the amount of time added/reduced by each factor

* Creates a disease outbreak event that allows admins to cause an outbreak of a virus of their choosing. Allows virus creation when choosing virus to give someone or for an outbreak.

* The normal base property values are now the defaults for disease creation

* Rebuild TGUI

* Rebuild TGUI

* Rebuild TGUI

* Update tgui.bundle.js

* remove redundant lines

* improves ui some and moves to using world time for analysis time

* fixes a bug with the analysis time and updates the initial known advanced disease list

* Buffs the disease outbreak event and adds a base stat row to the PANDEMIC

* Update tgui.bundle.js

* Implements calibration

* Adds a remove from database button

* Moves the known disease global list to work per z level

* Removes treatments from most chems and makes each instance of a symptom not acting purge some of the reagent that treated it

* Update symptoms.dm

* Adds stage to unknown diseases

* Moves accumulated error to work per z level and change the location of the delete strain data button

* Adds confirmation to the delete data button and moves the disease text out of the loop in the copy constructor

* fix indentation

* Replaces pent with hydrocodone in the advanced cure list

* gives more buffs to event disease based on severity. removes longevity from possible symptoms an event disease can get.  Fixes a bug with determining analysis time

* Update tgui.bundle.js

* Update pandemic.dm

* Update pandemic.dm

* Update tgui.bundle.js

* review changes

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* Update tgui.bundle.js

* review changes

* Update tgui.bundle.js

* Makes vaccines only add resistances and no longer cure

* improves pandemic ui and fixes calibration button not being properly disabled

* Update tgui.bundle.js

* Add the new agars to the virologist's fridge

* lowered evolution chance of viruses a bit

* further lowers evolution chance

* Update advance.dm

* Changes the scaling of analysis time and fixes stage speed presentation in the pandemic

* Scanners can now see virus strains that have been inserted in the pandemic

* Allows a mob to be infected by both an event and non event disease

* Fixes the +1 syringe of translocation stabbing your feet

* Update tgui.bundle.js

* Changes spontanous mutation to be per spread and makes disease events less likely.

* Diseases less common, mutations happen only on spread now, symptom list ordered alphabetically in the dropdown, fixed some bugs

* Update tgui.bundle.js

* changes virus alerts

* Removes numbers from the virus alert text and fixes a bug that caused excessive virus mutations

* Update tgui.bundle.js

* refactor disease spread

* Changes disease spread logic to give players options to protect themselves and others

* Blackbox things

* Increases announcement timer and fixes the infection talley

* Update disease_outbreak.dm

* Adds an incubation period to advanced viruses. bumps sneeze back to 5 range

* Adds failsafe to disease outbreaks that will infect a random crew member if none have arrived in 10 minutes

* Only record advanced disease infections

* Properly handle recording of disease infection events

* Changed resistance effect on cure

* another adjustment to res effect on cure

* Small resist buff, spontanous combustion buff and some calculation fixes

* changes spontanous combustion stat bonuses and maluses

* Update flesh_eating.dm

* Update flesh_eating.dm

* Update flesh_eating.dm

* Big trait changes and rebalance

* adds treatments to fire and necro

* Introduces viral contamination of food and reagent containers, as well as disinfection

* Fix runtime in reagent transfers

* Revert the prefs and config changes

* Slowed down diseases and made symptoms more gradual, improved disease alerts to both crew and dchat

* Sterilizine now sterilizes things contaminated with viruses. Heat reactions now take place alongside chemical reactions when adding reagents to a beaker

* Adds option to order sterile masks, goggles and biosuits in packs of 4. Makes sterile masks as good as internals for viruses

* adds logging to pandemic

* Changes symptom stats and increased disease varaiety

* Fixes some disease bugs

* Fixes some bugs and makes it behave better

* Adds shiver emote to shiver symptom

* Adds admin message/log to contracting an event disease and fixes copy behaviour when infecting

* Prefix spread defines

* Change the rest of the macros

* correct the disinfection temp macro

* Moves disease signals to their own file

* move disnifection temp back

* fix a type

* viral contaminations component review changes

* var name changes

* more style fixes

* Update tgui.bundle.js

* fixes pandemic

* Fixes disease outbreak having two carriers sometimes and changes the virus alert to the new one

* Update disease_defines.dm

* fixes samples not passing stages on properly

* actually fixes the bug

* Fixes stabilization being lost on cloning

* Finally completely and absolutely fixes the sample stages bug(please)

* Makes the pandemic a machine

* Update pandemic.dm

* removed drinks from cure requirements

* lowers chance of major viral outbreak

* fixes pandemic not processing properly

* Changes the cure system to have more options

* Makes mixing event viruses more random

* Fixes hardsuits having a 1% chance to be infected

* Increases virus protection of most clothing. medical scrubs and surgical hat buffed sunstantially

* Slow down progress of diseases

* makes spread less likely

* envirosuit is now slightly more protective from viruses, while the medical one is as good as scrubs

* Adds further protection to helmets

* Increases the number of possible cures and the scaling of required cures

* Pandemic ui improvements

* Update _disease.dm

* fix a bug with spread target in the disease outbreak event

* changes some clothing permeability

* Adds the ability to make viral DNA extracts by injecting a sample into a black slime core. It's equivalent to 2 stages

* Adds age to health analyzer, makes viral evolution toggle minor disabilities, confusion symptom now confuses more often

* Update pandemic.dm

* replace lazarus with acetic acid in the cures

* Changes the relation of the amount of cure options to required cures and the scaling of required cures with resistance

* Fixes virus renaming

* changes description and permeability of some medical jumpsuits

* Adds a list of all diseases infecting client mobs to the disease outbreak event

* uses event UID instead of ref in the disease

* Adds advanced disease carriers to admin antag menu

* Adds viral eraser which removes tracking and stabilizing. Admin spawn only for now

* Update tgui.bundle.js

* Adds the ability to create viral genetic material using radiation. it can be used in addition to that produced in xenobio

* changes alert logic, disease generation logic, adds treatments to weakness, cough and sneeze now more gradual and cough spreads at range 3

* makes disease advance a bit faster

* reduce time to announcement to 6 minutes after 3 people are infected

* Changes medibot disease detection to be the same as analyzers. Treatment chems now put the symptom on a cooldown that persists after they leave the body.

* Make sure the disease outbreak event only selects crew

* Fix abductor virus gland virus generation

* Adds sterilizine to viro locker

* Fixes null viruses appearing when merging virusless blood

* Adds oculine to hyphema treatments

* Rebalances weight loss and flesh eating

* Improvements to advanced disease carrier tab on the TGUI antag menu

* change the flag on away missions

* Update mob_spawn.dm

* Update tgui.bundle.js

* adds sterilizine recipe back

* Adds viral contamination to surgery tools and surgery steps

* small changes

* fixes pandemic ui. should work properly now(I hope)

* CI compliance

* Update flesh_eating.dm

* Update vomit.dm

* Update tgui.bundle.js

* Initial revision of analysis and fixes the UI issue with multiple stage samples

* refactors treatment and makes treatment chems more adjustable

* var correction

* symptoms and their contribution now show up on the pandemic

* Update tgui.bundle.js

* Update code/datums/diseases/advance/symptoms/cough.dm

Signed-off-by: Burzah <116982774+Burzah@users.noreply.github.com>

* change wizard disease and zombie disease macros to new ones

* Update tgui.bundle.js

* changes the part requirements on the pandemic boards to fit the actual parts

* fix misbehaviour when inserting samples without symptoms

* Some changes to difficulty scaling, reverts the level of projectile vomiting back to 4, and disallows germaphobes to avoid infection by injection

* Adds viral contamination to IV bags

---------

Signed-off-by: Burzah <116982774+Burzah@users.noreply.github.com>
Co-authored-by: Burzah <116982774+Burzah@users.noreply.github.com>

code/modules/reagents/reagent_containers/chemical_bottle.dm

@@ -302,6 +302,26 @@
 	desc = "A small bottle. Contains H0NI<42 virion culture in synthblood medium."
 	spawned_disease = /datum/disease/pierrot_throat
 
+/obj/item/reagent_containers/glass/bottle/tracking_agar
+	name = "Tracking agar bottle"
+	desc = "A small bottle. Contains tracking agar which allows modifying a virus without needing to reanalyze it"
+	list_reagents = list("tracking_agar" = 50)
+
+/obj/item/reagent_containers/glass/bottle/stable_agar
+	name = "Stable agar bottle"
+	desc = "A small bottle. Contains stable agar which stop a virus from being able to mutate on its own"
+	list_reagents = list("stable_agar" = 50)
+
+/obj/item/reagent_containers/glass/bottle/sterilizine
+	name = "Sterilizine bottle"
+	desc = "A small bottle. Contains sterilizine, which is used to sterilize beakers and syringes"
+	list_reagents = list("sterilizine" = 50)
+
+/obj/item/reagent_containers/glass/bottle/viral_eraser
+	name = "Viral eraser bottle"
+	desc = "A small bottle. Contains a small amount of viral eraser which removes all tracking and stabilizing from a virus"
+	list_reagents = list("viral_eraser" = 10)
+
 /obj/item/reagent_containers/glass/bottle/cold
 	name = "Rhinovirus culture bottle"
 	desc = "A small bottle. Contains XY-rhinovirus culture in synthblood medium."

code/modules/reagents/reagent_containers/glass_containers.dm

@@ -63,11 +63,20 @@
 				add_attack_logs(user, target, "Fed with [name] containing [contained]", !!target.ckey ? null : ATKLOG_ALL)
 			else
 				to_chat(user, "<span class='notice'>You swallow a gulp of [src].</span>")
-
 			var/fraction = min(5 / reagents.total_volume, 1)
 			reagents.reaction(target, REAGENT_INGEST, fraction)
 			addtimer(CALLBACK(reagents, TYPE_PROC_REF(/datum/reagents, trans_to), target, 5), 5)
 			playsound(target.loc,'sound/items/drink.ogg', rand(10,50), TRUE)
+			// Add viruses where needed
+			if(length(target.viruses))
+				AddComponent(/datum/component/viral_contamination, target.viruses)
+			// Infect contained blood as well for splash reactions
+			var/datum/reagent/blood/blood_contained = locate() in reagents.reagent_list
+			if(blood_contained?.data["viruses"])
+				var/list/blood_viruses = blood_contained.data["viruses"]
+				blood_viruses |= target.viruses.Copy()
+				blood_contained.data["viruses"] = blood_viruses
+			SEND_SIGNAL(src, COMSIG_MOB_REAGENT_EXCHANGE, target)
 
 /obj/item/reagent_containers/glass/normal_act(atom/target, mob/living/user)
 	if(!check_allowed_items(target, target_self = TRUE) || !is_open_container() || !reagents)

code/modules/reagents/reagent_containers/iv_bag.dm

@@ -54,6 +54,8 @@
 
 /obj/item/reagent_containers/iv_bag/proc/begin_processing(mob/target)
 	injection_target = target
+	if(target.viruses)
+		AddComponent(/datum/component/viral_contamination, target.viruses)
 	RegisterSignal(injection_target, COMSIG_PARENT_EXAMINE, PROC_REF(on_examine))
 	START_PROCESSING(SSobj, src)
 	update_iv_type()

code/modules/reagents/reagent_containers/syringes.dm

@@ -188,6 +188,10 @@
 	var/fraction = min(amount_per_transfer_from_this / reagents.total_volume, 1)
 	reagents.reaction(target, REAGENT_INGEST, fraction)
 	reagents.trans_to(target, amount_per_transfer_from_this)
+	if(iscarbon(target))
+		var/mob/living/carbon/carbon_target = target
+		if(length(carbon_target.viruses))
+			AddComponent(/datum/component/viral_contamination, carbon_target.viruses)
 	to_chat(user, "<span class='notice'>You inject [amount_per_transfer_from_this] units of the solution. The syringe now contains [reagents.total_volume] units.</span>")
 	if(reagents.total_volume <= 0 && mode == SYRINGE_INJECT)
 		mode = SYRINGE_DRAW