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/events/disease_outbreak.dm

@@ -1,5 +1,9 @@
 GLOBAL_LIST_EMPTY(current_pending_diseases)
 /datum/event/disease_outbreak
+	// We only want the announcement to happen after the virus has spawned on station
+	announceWhen = -1
+	// Keep the event running until we announce it
+	noAutoEnd = TRUE
 	/// The type of disease that patient zero will be infected with.
 	var/datum/disease/chosen_disease
 
@@ -11,6 +15,8 @@ GLOBAL_LIST_EMPTY(current_pending_diseases)
 	var/static/list/transmissable_symptoms = list()
 	var/static/list/diseases_minor = list()
 	var/static/list/diseases_moderate_major = list()
+	var/force_disease_time = 300
+	var/list/infected_players = list()
 
 /datum/event/disease_outbreak/setup()
 	if(isemptylist(diseases_minor) && isemptylist(diseases_moderate_major))
@@ -18,49 +24,90 @@ GLOBAL_LIST_EMPTY(current_pending_diseases)
 	if(isemptylist(transmissable_symptoms))
 		populate_symptoms()
 	var/datum/disease/virus
-	if(prob(50))
-		switch(severity)
-			if(EVENT_LEVEL_MUNDANE)
-				virus = pick(diseases_minor)
-			if(EVENT_LEVEL_MODERATE)
+	// Either choose a type to create a normal disease from or create an advanced disease
+	switch(severity)
+		if(EVENT_LEVEL_MUNDANE)
+			virus = pick(diseases_minor)
+		if(EVENT_LEVEL_MODERATE)
+			if(prob(50))
 				virus = pick(diseases_moderate_major)
 			else
-				stack_trace("Disease Outbreak: Invalid Event Level [severity]. Expected: 1-2")
-				virus = /datum/disease/cold
-		chosen_disease = new virus()
-	else
-		if(severity == EVENT_LEVEL_MODERATE)
-			chosen_disease = create_virus(severity * pick(2,3))	//50% chance for a major disease instead of a moderate one
-		else
+				chosen_disease = create_virus(severity * 2)
+		if(EVENT_LEVEL_MAJOR)
 			chosen_disease = create_virus(severity * 2)
+	if(virus)
+		chosen_disease = new virus
 
 	chosen_disease.carrier = TRUE
 
 /datum/event/disease_outbreak/start()
-	GLOB.current_pending_diseases += chosen_disease
+	GLOB.current_pending_diseases += list(list("disease" = chosen_disease, "event" = src))
 	for(var/mob/M as anything in GLOB.dead_mob_list) //Announce outbreak to dchat
 		if(istype(chosen_disease, /datum/disease/advance))
-			var/datum/disease/advance/temp_disease = chosen_disease.Copy()
-			to_chat(M, "<span class='deadsay'><b>Disease outbreak:</b> The next new arrival is a carrier of [chosen_disease.name]! A \"[chosen_disease.severity]\" disease with the following symptoms: [english_list(temp_disease.symptoms)]</span>")
+			var/datum/disease/advance/temp_disease = chosen_disease
+			to_chat(M, chat_box_examine("<span class='deadsay'><b>Disease outbreak:</b> The next new arrival is a carrier of [chosen_disease.name]! A \"[chosen_disease.severity]\" disease with the following symptoms:\n[english_list(temp_disease.symptoms)]\nand the following stats:\n[english_map(temp_disease.GenerateProperties())]</span>"))
 		else
-			to_chat(M, "<span class='deadsay'><b>Disease outbreak:</b> The next new arrival is a carrier of a \"[chosen_disease.severity]\" disease: [chosen_disease.name]!</span>")
+			to_chat(M, chat_box_examine("<span class='deadsay'><b>Disease outbreak:</b> The next new arrival is a carrier of a \"[chosen_disease.severity]\" disease: [chosen_disease.name]!</span>"))
+
+/datum/event/disease_outbreak/announce()
+	switch(severity)
+		if(EVENT_LEVEL_MAJOR)
+			GLOB.major_announcement.Announce("Lethal viral pathogen detected aboard [station_name()]. All personnel must contain the outbreak.", "Biohazard Alert", 'sound/effects/siren-spooky.ogg', new_sound2 = 'sound/AI/outbreak_virus.ogg')
+		if(EVENT_LEVEL_MODERATE)
+			GLOB.minor_announcement.Announce("Moderate contagion detected aboard [station_name()].", new_sound = 'sound/misc/notice2.ogg', new_title = "Contagion Alert")
+		if(EVENT_LEVEL_MUNDANE)
+			GLOB.minor_announcement.Announce("Minor contagion detected aboard [station_name()].", new_sound = 'sound/misc/notice2.ogg', new_title = "Contagion Alert")
+	// We did our announcement, the event no longer needs to run
+	kill()
+
+/datum/event/disease_outbreak/process()
+	if(activeFor == force_disease_time)
+		for(var/list/disease_event in GLOB.current_pending_diseases)
+			if(chosen_disease == disease_event["disease"])
+				for(var/mob/living/carbon/human/player in GLOB.player_list)
+					if((player.name in  GLOB.crew_list) && player.ForceContractDisease(chosen_disease, TRUE, TRUE))
+						GLOB.current_pending_diseases -= list(disease_event)
+						break
+				break
+	if(length(infected_players) > 2 && announceWhen <= 0)
+		announceWhen = activeFor + 180
+	. = ..()
 
 //Creates a virus with a harmful effect, guaranteed to be spreadable by contact or airborne
 /datum/event/disease_outbreak/proc/create_virus(max_severity = 6)
-	var/datum/disease/advance/A = new /datum/disease/advance
-	A.symptoms = A.GenerateSymptomsBySeverity(max_severity - 1, max_severity, 2) //Choose "Payload" symptoms
-	A.AssignProperties(A.GenerateProperties())
-	var/list/symptoms_to_try = transmissable_symptoms.Copy()
-	while(length(symptoms_to_try))
-		if(A.spread_text != "Blood")
-			break
-		if(length(A.symptoms) < VIRUS_SYMPTOM_LIMIT)	//Ensure the virus is spreadable by adding symptoms that boost transmission
-			var/datum/symptom/TS = pick_n_take(symptoms_to_try)
-			A.AddSymptom(new TS)
-		else
-			popleft(A.symptoms)	//We have a full symptom list but are still not transmittable. Try removing one of the "payloads"
+	var/datum/disease/advance/A = new /datum/disease/advance(_event = UID())
+	A.clear_symptoms()
+	// Base properties get buffs depending on severity
+	var/list/properties_to_buff = A.base_properties.Copy() - list("transmissibility")
+	for(var/i = 0, i < max_severity / 2, i++)
+		A.base_properties[pick(properties_to_buff)]++
+	A.base_properties["stealth"] += max_severity // Stealth gets an additional bonus since most symptoms reduce it a fair bit.
+	var/spread_threhsold = 4
+	// Chance for it to be extra spready, scales quadratically with severity
+	if(prob((max_severity ** 2) * 3))
+		spread_threhsold = 5
+	if(prob((max_severity ** 2) * 1.5))
+		spread_threhsold = 6
+
+	// If we have extra spread include either cough or sneeze
+	if(spread_threhsold >= 5)
+		var/symptom_path = pick(/datum/symptom/cough, /datum/symptom/sneeze)
+		A.add_symptom_path(symptom_path)
+
+	// Generate payload. 2-3 symptoms that actually do something
+	A.symptoms += A.GenerateSymptomsBySeverity(max_severity - 1, max_severity, 1)
+	A.symptoms += A.GenerateSymptomsBySeverity(max_severity - 3, max_severity - 1, rand(1, 2))
+
+	var/symptom_list = transmissable_symptoms.Copy()
+
+	// Add symptoms that increase transmittability to fill the rest
+	while(length(A.symptoms) < VIRUS_SYMPTOM_LIMIT)
+		var/symptom_path = pick_n_take(symptom_list)
+		A.add_symptom_path(symptom_path)
+
+	// Add extra transmissibility through base properties as needed
+	A.base_properties["transmissibility"] = max(0, spread_threhsold - (A.totaltransmissibility() - length(A.symptoms)))
 
-		A.AssignProperties(A.GenerateProperties())
 	A.name = pick(GLOB.alphabet_uppercase) + num2text(rand(1,9)) + pick(GLOB.alphabet_uppercase) + num2text(rand(1,9)) + pick("v", "V", "-" + num2text(GLOB.game_year), "")
 	A.Refresh()
 	return A
@@ -71,13 +118,15 @@ GLOBAL_LIST_EMPTY(current_pending_diseases)
 		if(is_type_in_list(CD, disease_blacklist))
 			continue
 		switch(CD.severity)
-			if(NONTHREAT, MINOR)
+			if(VIRUS_NONTHREAT, VIRUS_MINOR)
 				diseases_minor += candidate
-			if(MEDIUM, HARMFUL, DANGEROUS, BIOHAZARD)
+			if(VIRUS_MEDIUM, VIRUS_HARMFUL, VIRUS_DANGEROUS, VIRUS_BIOHAZARD)
 				diseases_moderate_major += candidate
 
 /datum/event/disease_outbreak/proc/populate_symptoms()
-	for(var/candidate in subtypesof(/datum/symptom))
+	// Disease events shouldn't just resolve themselves
+	var/list/candidate_list = subtypesof(/datum/symptom) - /datum/symptom/heal/longevity
+	for(var/candidate in candidate_list)
 		var/datum/symptom/CS = candidate
-		if(initial(CS.transmittable) > 1)
+		if(initial(CS.transmissibility) > 0)
 			transmissable_symptoms += candidate

code/modules/events/event_container.dm

@@ -209,7 +209,8 @@ GLOBAL_LIST_EMPTY(event_last_fired)
 		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Slaughter Demon",		/datum/event/spawn_slaughter,	20,  	is_one_shot = TRUE),
 		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Shadow Demon", 		/datum/event/spawn_slaughter/shadow,	20, 	is_one_shot = TRUE),
 		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Demonic Incursion", 	/datum/event/demon_incursion, 	20,		list(ASSIGNMENT_SECURITY = 3)),
-		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Immovable Rod",		/datum/event/immovable_rod,				0,		list(ASSIGNMENT_ENGINEER = 10), TRUE)
+		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Immovable Rod",		/datum/event/immovable_rod,				0,		list(ASSIGNMENT_ENGINEER = 10), TRUE),
+		new /datum/event_meta(EVENT_LEVEL_MAJOR, "Disease Outbreak",			/datum/event/disease_outbreak, 			15,		list(ASSIGNMENT_MEDICAL = 4), TRUE),
 		//new /datum/event_meta(EVENT_LEVEL_MAJOR, "Floor Cluwne",	/datum/event/spawn_floor_cluwne,	15, is_one_shot = TRUE)
 		//new /datum/event_meta(EVENT_LEVEL_MAJOR, "Pulse Demon Infiltration",	/datum/event/spawn_pulsedemon,	20,	is_one_shot = TRUE)
 	)