Proper mirror PR for the disease refactor because I fucked up the first one. (#2026)

* Revert "im a dumbass and didn't see the .rej files Revert "[MIRROR] Disease Refactor" (#2025)"

This reverts commit 44742cb115.

* Delete shuttle_loan.dm.rej

* Delete life.dm.rej

* Update life.dm

* Delete life.dm.rej

* compile

code/modules/admin/secrets.dm

@@ -149,8 +149,9 @@
 			var/choice = input("Are you sure you want to cure all disease?") in list("Yes", "Cancel")
 			if(choice == "Yes")
 				message_admins("[key_name_admin(usr)] has cured all diseases.")
-				for(var/datum/disease/D in SSdisease.processing)
-					D.cure(D)
+				for(var/thing in SSdisease.active_diseases)
+					var/datum/disease/D = thing
+					D.cure(0)
 		if("set_name")
 			if(!check_rights(R_ADMIN))
 				return

code/modules/admin/verbs/randomverbs.dm

@@ -615,7 +615,7 @@ Traitors and the like can also be revived with the previous role mostly intact.
 	message_admins("[key_name_admin(usr)] has gibbed [key_name_admin(M)]")
 
 	if(isobserver(M))
-		new /obj/effect/gibspawner/generic(M.loc, M.viruses)
+		new /obj/effect/gibspawner/generic(get_turf(M))
 		return
 	if(confirm == "Yes")
 		M.gib()

code/modules/clothing/ears/ears.dm

@@ -47,4 +47,4 @@
 		H.update_inv_ears()
 		H.update_inv_neck()
 		H.update_inv_head()
-	to_chat(owner, "<span class='notice'>You turn the music [headphones_on? "on. Untz Untz Untz!" : "off."]</span>")
+	to_chat(owner, "<span class='notice'>You turn the music [headphones_on? "on. Untz Untz Untz!" : "off."]</span>")

code/modules/events/disease_outbreak.dm

@@ -27,11 +27,17 @@
 			continue
 		if(T.z != ZLEVEL_STATION)
 			continue
-		var/foundAlready = 0	// don't infect someone that already has the virus
-		for(var/datum/disease/D in H.viruses)
-			foundAlready = 1
+		if(!H.client)
+			continue
+		if(H.stat == DEAD)
+			continue
+		if(VIRUSIMMUNE in H.dna.species.species_traits) //Don't pick someone who's virus immune, only for it to not do anything.
+			continue
+		var/foundAlready = FALSE	// don't infect someone that already has a disease
+		for(var/thing in H.viruses)
+			foundAlready = TRUE
 			break
-		if(H.stat == DEAD || foundAlready)
+		if(foundAlready)
 			continue
 
 		var/datum/disease/D
@@ -45,6 +51,6 @@
 			DS.strain_data["SE"] = H.dna.struc_enzymes
 		else
 			D = new virus_type()
-		D.carrier = 1
+		D.carrier = TRUE
 		H.AddDisease(D)
 		break

code/modules/events/shuttle_loan.dm

@@ -135,7 +135,7 @@
 					new /obj/structure/spider/stickyweb(T)
 
 			if(ANTIDOTE_NEEDED)
-				var/virus_type = pick(/datum/disease/beesease, /datum/disease/brainrot, /datum/disease/fluspanish)
+				var/obj/item/weapon/reagent_containers/glass/bottle/virus_type = pick(/obj/item/weapon/reagent_containers/glass/bottle/beesease, /obj/item/weapon/reagent_containers/glass/bottle/brainrot, /obj/item/weapon/reagent_containers/glass/bottle/fluspanish)
 				var/turf/T
 				for(var/i=0, i<10, i++)
 					if(prob(15))
@@ -145,11 +145,7 @@
 					else if(prob(25))
 						shuttle_spawns.Add(/obj/item/weapon/shard)
 					T = pick_n_take(empty_shuttle_turfs)
-					var/obj/effect/decal/cleanable/blood/b = new(T)
-					var/datum/disease/D = new virus_type()
-					D.longevity = 1000
-					b.viruses += D
-					D.holder = b
+					new virus_type(T)
 				shuttle_spawns.Add(/obj/structure/closet/crate)
 				shuttle_spawns.Add(/obj/item/weapon/reagent_containers/glass/bottle/pierrot_throat)
 				shuttle_spawns.Add(/obj/item/weapon/reagent_containers/glass/bottle/magnitis)

code/modules/events/spontaneous_appendicitis.dm

@@ -8,10 +8,17 @@
 
 /datum/round_event/spontaneous_appendicitis/start()
 	for(var/mob/living/carbon/human/H in shuffle(GLOB.living_mob_list))
-		var/foundAlready = 0	//don't infect someone that already has the virus
-		for(var/datum/disease/D in H.viruses)
-			foundAlready = 1
-		if(H.stat == 2 || foundAlready)
+		if(!H.client)
+			continue
+		if(H.stat == DEAD)
+			continue
+		if(!H.getorgan(/obj/item/organ/appendix)) //Don't give the disease to some who lacks it, only for it to be auto-cured
+			continue
+		var/foundAlready = FALSE	//don't infect someone that already has appendicitis
+		for(var/datum/disease/appendicitis/A in H.viruses)
+			foundAlready = TRUE
+			break
+		if(foundAlready)
 			continue
 
 		var/datum/disease/D = new /datum/disease/appendicitis

code/modules/food_and_drinks/kitchen_machinery/processor.dm

@@ -162,7 +162,8 @@
 	//set reagent data
 	B.data["donor"] = O
 
-	for(var/datum/disease/D in O.viruses)
+	for(var/thing in O.viruses)
+		var/datum/disease/D = thing
 		if(!(D.spread_flags & SPECIAL))
 			B.data["viruses"] += D.Copy()
 	if(O.has_dna())

code/modules/mob/living/blood.dm

@@ -137,7 +137,8 @@
 		if(blood_id == C.get_blood_id())//both mobs have the same blood substance
 			if(blood_id == "blood") //normal blood
 				if(blood_data["viruses"])
-					for(var/datum/disease/D in blood_data["viruses"])
+					for(var/thing in blood_data["viruses"])
+						var/datum/disease/D = thing
 						if((D.spread_flags & SPECIAL) || (D.spread_flags & NON_CONTAGIOUS))
 							continue
 						C.ForceContractDisease(D)
@@ -162,7 +163,8 @@
 		blood_data["donor"] = src
 		blood_data["viruses"] = list()
 
-		for(var/datum/disease/D in viruses)
+		for(var/thing in viruses)
+			var/datum/disease/D = thing
 			blood_data["viruses"] += D.Copy()
 
 		blood_data["blood_DNA"] = copytext(dna.unique_enzymes,1,0)

code/modules/mob/living/carbon/alien/death.dm

@@ -1,8 +1,8 @@
 /mob/living/carbon/alien/spawn_gibs(with_bodyparts)
 	if(with_bodyparts)
-		new /obj/effect/gibspawner/xeno(loc,viruses)
+		new /obj/effect/gibspawner/xeno(get_turf(src))
 	else
-		new /obj/effect/gibspawner/xenobodypartless(loc,viruses)
+		new /obj/effect/gibspawner/xenobodypartless(get_turf(src))
 
 /mob/living/carbon/alien/gib_animation()
 	new /obj/effect/temp_visual/gib_animation(loc, "gibbed-a")

code/modules/mob/living/carbon/alien/larva/death.dm

@@ -8,9 +8,9 @@
 
 /mob/living/carbon/alien/larva/spawn_gibs(with_bodyparts)
 	if(with_bodyparts)
-		new /obj/effect/gibspawner/larva(loc,viruses)
+		new /obj/effect/gibspawner/larva(get_turf(src))
 	else
-		new /obj/effect/gibspawner/larvabodypartless(loc,viruses)
+		new /obj/effect/gibspawner/larvabodypartless(get_turf(src))
 
 /mob/living/carbon/alien/larva/gib_animation()
 	new /obj/effect/temp_visual/gib_animation(loc, "gibbed-l")

code/modules/mob/living/carbon/carbon.dm

@@ -716,8 +716,9 @@
 	var/obj/item/organ/brain/B = getorgan(/obj/item/organ/brain)
 	if(B)
 		B.damaged_brain = 0
-	for(var/datum/disease/D in viruses)
-		if (D.severity != NONTHREAT)
+	for(var/thing in viruses)
+		var/datum/disease/D = thing
+		if(D.severity != NONTHREAT)
 			D.cure(0)
 	if(admin_revive)
 		regenerate_limbs()

code/modules/mob/living/carbon/carbon_defense.dm

@@ -111,11 +111,13 @@
 
 /mob/living/carbon/attack_hand(mob/living/carbon/human/user)
 
-	for(var/datum/disease/D in viruses)
+	for(var/thing in viruses)
+		var/datum/disease/D = thing
 		if(D.IsSpreadByTouch())
 			user.ContractDisease(D)
 
-	for(var/datum/disease/D in user.viruses)
+	for(var/thing in user.viruses)
+		var/datum/disease/D = thing
 		if(D.IsSpreadByTouch())
 			ContractDisease(D)
 
@@ -128,11 +130,13 @@
 
 
 /mob/living/carbon/attack_paw(mob/living/carbon/monkey/M)
-	for(var/datum/disease/D in viruses)
+	for(var/thing in viruses)
+		var/datum/disease/D = thing
 		if(D.IsSpreadByTouch())
 			M.ContractDisease(D)
 
-	for(var/datum/disease/D in M.viruses)
+	for(var/thing in M.viruses)
+		var/datum/disease/D = thing
 		if(D.IsSpreadByTouch())
 			ContractDisease(D)
 
@@ -141,7 +145,8 @@
 		return 0
 
 	if(..()) //successful monkey bite.
-		for(var/datum/disease/D in M.viruses)
+		for(var/thing in M.viruses)
+			var/datum/disease/D = thing
 			ForceContractDisease(D)
 		return 1
 

code/modules/mob/living/carbon/human/death.dm

@@ -6,9 +6,9 @@
 
 /mob/living/carbon/human/spawn_gibs(with_bodyparts)
 	if(with_bodyparts)
-		new /obj/effect/gibspawner/human(loc, viruses, dna)
+		new /obj/effect/gibspawner/human(get_turf(src), dna)
 	else
-		new /obj/effect/gibspawner/humanbodypartless(loc, viruses, dna)
+		new /obj/effect/gibspawner/humanbodypartless(get_turf(src), dna)
 
 /mob/living/carbon/human/spawn_dust(just_ash = FALSE)
 	if(just_ash)

code/modules/mob/living/carbon/human/human.dm

@@ -131,7 +131,8 @@
 				//Virsuses
 				if(viruses.len)
 					stat("Viruses:", null)
-					for(var/datum/disease/D in viruses)
+					for(var/thing in viruses)
+						var/datum/disease/D = thing
 						stat("*", "[D.name], Type: [D.spread_text], Stage: [D.stage]/[D.max_stages], Possible Cure: [D.cure_text]")
 
 

code/modules/mob/living/carbon/life.dm

@@ -224,6 +224,15 @@
 /mob/living/carbon/proc/handle_blood()
 	return
 
+/mob/living/carbon/handle_diseases()
+	for(var/thing in viruses)
+		var/datum/disease/D = thing
+		if(prob(D.infectivity))
+			D.spread()
+
+		if(stat != DEAD)
+			D.stage_act()
+
 /mob/living/carbon/proc/handle_changeling()
 	if(mind && hud_used && hud_used.lingchemdisplay)
 		if(mind.changeling)

code/modules/mob/living/death.dm

@@ -18,7 +18,7 @@
 	return
 
 /mob/living/proc/spawn_gibs()
-	new /obj/effect/gibspawner/generic(loc, viruses)
+	new /obj/effect/gibspawner/generic(get_turf(src))
 
 /mob/living/proc/spill_organs()
 	return

code/modules/mob/living/life.dm

@@ -18,12 +18,16 @@
 			return
 	var/datum/gas_mixture/environment = loc.return_air()
 
-	if(stat != DEAD)
-		//Breathing, if applicable
-		handle_breathing(times_fired)
 	if(stat != DEAD)
 		//Mutations and radiation
 		handle_mutations_and_radiation()
+
+	if(stat != DEAD)
+		//Breathing, if applicable
+		handle_breathing(times_fired)
+
+	handle_diseases() // DEAD check is in the proc itself; we want it to spread even if the mob is dead, but to handle its disease-y properties only if you're not.
+
 	if(stat != DEAD)
 		//Random events (vomiting etc)
 		handle_random_events()
@@ -60,6 +64,9 @@
 	radiation = 0 //so radiation don't accumulate in simple animals
 	return
 
+/mob/living/proc/handle_diseases()
+	return
+
 /mob/living/proc/handle_diginvis()
 	if(!digitaldisguise)
 		src.digitaldisguise = image(loc = src)

code/modules/mob/living/silicon/death.dm

@@ -1,5 +1,5 @@
 /mob/living/silicon/spawn_gibs()
-	new /obj/effect/gibspawner/robot(loc,viruses)
+	new /obj/effect/gibspawner/robot(get_turf(src))
 
 /mob/living/silicon/spawn_dust()
 	new /obj/effect/decal/remains/robot(loc)

code/modules/mob/living/silicon/pai/software.dm

@@ -513,7 +513,8 @@
 		Structural Integrity: [M.getBruteLoss() > 50 ? "<font color=#FF5555>" : "<font color=#55FF55>"][M.getBruteLoss()]</font><br>
 		Body Temperature: [M.bodytemperature-T0C]&deg;C ([M.bodytemperature*1.8-459.67]&deg;F)<br>
 		"}
-		for(var/datum/disease/D in M.viruses)
+		for(var/thing in M.viruses)
+			var/datum/disease/D = thing
 			dat += {"<h4>Infection Detected.</h4><br>
 					 Name: [D.name]<br>
 					 Type: [D.spread_text]<br>

code/modules/mob/living/simple_animal/bot/medbot.dm

@@ -373,7 +373,8 @@
 		return 1
 
 	if(treat_virus && !C.reagents.has_reagent(treatment_virus_avoid) && !C.reagents.has_reagent(treatment_virus))
-		for(var/datum/disease/D in C.viruses)
+		for(var/thing in C.viruses)
+			var/datum/disease/D = thing
 			//the medibot can't detect viruses that are undetectable to Health Analyzers or Pandemic machines.
 			if(!(D.visibility_flags & HIDDEN_SCANNER || D.visibility_flags & HIDDEN_PANDEMIC) \
 			&& D.severity != NONTHREAT \
@@ -424,7 +425,8 @@
 	else
 		if(treat_virus)
 			var/virus = 0
-			for(var/datum/disease/D in C.viruses)
+			for(var/thing in C.viruses)
+				var/datum/disease/D = thing
 				//detectable virus
 				if((!(D.visibility_flags & HIDDEN_SCANNER)) || (!(D.visibility_flags & HIDDEN_PANDEMIC)))
 					if(D.severity != NONTHREAT)      //virus is harmful

code/modules/mob/mob.dm

@@ -11,8 +11,7 @@
 	qdel(hud_used)
 	if(mind && mind.current == src)
 		spellremove(src)
-	for(var/infection in viruses)
-		qdel(infection)
+	QDEL_LIST(viruses)
 	for(var/cc in client_colours)
 		qdel(cc)
 	client_colours = null

code/modules/mob/mob_defines.dm

@@ -113,7 +113,7 @@
 
 //List of active diseases
 
-	var/list/viruses = list() // replaces var/datum/disease/virus
+	var/list/viruses = list() // list of all diseases in a mob
 	var/list/resistances = list()
 
 	mouse_drag_pointer = MOUSE_ACTIVE_POINTER

code/modules/mob/transform_procs.dm

@@ -65,9 +65,9 @@
 	if (tr_flags & TR_KEEPVIRUS)
 		O.viruses = viruses
 		viruses = list()
-		for(var/datum/disease/D in O.viruses)
+		for(var/thing in O.viruses)
+			var/datum/disease/D = thing
 			D.affected_mob = O
-			D.holder = O
 
 	//keep damage?
 	if (tr_flags & TR_KEEPDAMAGE)
@@ -219,9 +219,9 @@
 	if (tr_flags & TR_KEEPVIRUS)
 		O.viruses = viruses
 		viruses = list()
-		for(var/datum/disease/D in O.viruses)
+		for(var/thing in O.viruses)
+			var/datum/disease/D = thing
 			D.affected_mob = O
-			D.holder = O
 		O.med_hud_set_status()
 
 	//keep damage?

code/modules/reagents/chemistry/machinery/pandemic.dm

@@ -150,7 +150,7 @@
 				if(!new_name || ..())
 					return
 				A.AssignName(new_name)
-				for(var/datum/disease/advance/AD in SSdisease.processing)
+				for(var/datum/disease/advance/AD in SSdisease.active_diseases)
 					AD.Refresh()
 				. = TRUE
 		if("create_culture_bottle")

code/modules/reagents/chemistry/reagents/medicine_reagents.dm

@@ -58,13 +58,11 @@
 	M.confused = 0
 	M.SetSleeping(0, 0)
 	M.jitteriness = 0
-	for(var/datum/disease/D in M.viruses)
+	for(var/thing in M.viruses)
+		var/datum/disease/D = thing
 		if(D.severity == NONTHREAT)
 			continue
-		D.spread_text = "Remissive"
-		D.stage--
-		if(D.stage < 1)
-			D.cure()
+		D.cure()
 	..()
 	. = 1
 
@@ -686,7 +684,7 @@
 	taste_description = "dull toxin"
 
 /datum/reagent/medicine/oculine/on_mob_life(mob/living/M)
-	var/obj/item/organ/eyes/eyes = M.getorganslot("eye_sight")
+	var/obj/item/organ/eyes/eyes = M.getorganslot("eyes_sight")
 	if (!eyes)
 		return
 	if(M.disabilities & BLIND)

code/modules/reagents/chemistry/reagents/other_reagents.dm

@@ -13,7 +13,8 @@
 
 /datum/reagent/blood/reaction_mob(mob/M, method=TOUCH, reac_volume)
 	if(data && data["viruses"])
-		for(var/datum/disease/D in data["viruses"])
+		for(var/thing in data["viruses"])
+			var/datum/disease/D = thing
 
 			if((D.spread_flags & SPECIAL) || (D.spread_flags & NON_CONTAGIOUS))
 				continue
@@ -73,11 +74,6 @@
 	if(data["blood_DNA"])
 		B.blood_DNA[data["blood_DNA"]] = data["blood_type"]
 
-	for(var/datum/disease/D in data["viruses"])
-		var/datum/disease/newVirus = D.Copy(1)
-		B.viruses += newVirus
-		newVirus.holder = B
-
 
 /datum/reagent/liquidgibs
 	name = "Liquid gibs"
@@ -96,7 +92,8 @@
 
 /datum/reagent/vaccine/reaction_mob(mob/M, method=TOUCH, reac_volume)
 	if(islist(data) && (method == INGEST || method == INJECT))
-		for(var/datum/disease/D in M.viruses)
+		for(var/thing in M.viruses)
+			var/datum/disease/D = thing
 			if(D.GetDiseaseID() in data)
 				D.cure()
 		M.resistances |= data