Disease Refactor (#2021)

code/_onclick/other_mobs.dm

@@ -100,7 +100,8 @@
 							"<span class='userdanger'>[name] bites [ML]!</span>")
 			if(armor >= 2)
 				return
-			for(var/datum/disease/D in viruses)
+			for(var/thing in viruses)
+				var/datum/disease/D = thing
 				ML.ForceContractDisease(D)
 		else
 			ML.visible_message("<span class='danger'>[src] has attempted to bite [ML]!</span>")

code/controllers/subsystem/disease.dm

@@ -1,11 +1,8 @@
 SUBSYSTEM_DEF(disease)
 	name = "Disease"
-	flags = SS_KEEP_TIMING|SS_NO_INIT
-	runlevels = RUNLEVEL_GAME | RUNLEVEL_POSTGAME
-
-	var/list/currentrun = list()
-	var/list/processing = list()
+	flags = SS_NO_FIRE
 
+	var/list/active_diseases = list() //List of Active disease in all mobs; purely for quick referencing.
 	var/list/diseases
 	var/list/archive_diseases = list()
 
@@ -15,27 +12,5 @@ SUBSYSTEM_DEF(disease)
 	if(!diseases)
 		diseases = subtypesof(/datum/disease)
 
-/datum/controller/subsystem/disease/Recover()
-	currentrun = SSdisease.currentrun
-	processing = SSdisease.processing
-	diseases = SSdisease.diseases
-	archive_diseases = SSdisease.archive_diseases
-
 /datum/controller/subsystem/disease/stat_entry(msg)
-	..("P:[processing.len]")
-
-/datum/controller/subsystem/disease/fire(resumed = 0)
-	if(!resumed)
-		src.currentrun = processing.Copy()
-	//cache for sanic speed (lists are references anyways)
-	var/list/currentrun = src.currentrun
-
-	while(currentrun.len)
-		var/datum/thing = currentrun[currentrun.len]
-		currentrun.len--
-		if(thing)
-			thing.process()
-		else
-			processing.Remove(thing)
-		if (MC_TICK_CHECK)
-			return
+	..("P:[active_diseases.len]")

code/datums/diseases/_MobProcs.dm

@@ -1,6 +1,7 @@
 
 /mob/proc/HasDisease(datum/disease/D)
-	for(var/datum/disease/DD in viruses)
+	for(var/thing in viruses)
+		var/datum/disease/DD = thing
 		if(D.IsSame(DD))
 			return 1
 	return 0
@@ -39,7 +40,7 @@
 		var/datum/disease/DD = new D.type(1, D, 0)
 		viruses += DD
 		DD.affected_mob = src
-		DD.holder = src
+		SSdisease.active_diseases += DD //Add it to the active diseases list, now that it's actually in a mob and being processed.
 
 		//Copy properties over. This is so edited diseases persist.
 		var/list/skipped = list("affected_mob","holder","carrier","stage","type","parent_type","vars","transformed")
@@ -147,6 +148,9 @@
 
 
 /mob/living/carbon/human/CanContractDisease(datum/disease/D)
-	if(dna && (VIRUSIMMUNE in dna.species.species_traits))
+	if(dna && (VIRUSIMMUNE in dna.species.species_traits) && !D.bypasses_immunity)
 		return 0
+	for(var/thing in D.required_organs)
+		if(!((locate(thing) in bodyparts) || (locate(thing) in internal_organs)))
+			return 0
 	return ..()

code/datums/diseases/_disease.dm

@@ -46,21 +46,23 @@
 	var/stage_prob = 4
 
 	//Other
-	var/longevity = 150 //Time in ticks disease stays in objects, Syringes and such are infinite.
 	var/list/viable_mobtypes = list() //typepaths of viable mobs
 	var/mob/living/carbon/affected_mob = null
-	var/atom/movable/holder = null
 	var/list/cures = list() //list of cures if the disease has the CURABLE flag, these are reagent ids
 	var/infectivity = 65
 	var/cure_chance = 8
-	var/carrier = 0 //If our host is only a carrier
+	var/carrier = FALSE //If our host is only a carrier
+	var/bypasses_immunity = FALSE //Does it skip species virus immunity check? Some things may diseases and not viruses
 	var/permeability_mod = 1
 	var/severity =	NONTHREAT
 	var/list/required_organs = list()
 	var/needs_all_cures = TRUE
 	var/list/strain_data = list() //dna_spread special bullshit
 
-
+/datum/disease/Destroy()
+	affected_mob = null
+	SSdisease.active_diseases.Remove(src)
+	return ..()
 
 /datum/disease/proc/stage_act()
 	var/cure = has_cure()
@@ -93,13 +95,16 @@
 	if(!. || (needs_all_cures && . < cures.len))
 		return 0
 
-/datum/disease/proc/spread(atom/source, force_spread = 0)
+
+/datum/disease/proc/spread(force_spread = 0)
+	if(!affected_mob)
+		return
+
 	if((spread_flags & SPECIAL || spread_flags & NON_CONTAGIOUS || spread_flags & BLOOD) && !force_spread)
 		return
 
-	if(affected_mob)
-		if( affected_mob.reagents.has_reagent("spaceacillin") || (affected_mob.satiety > 0 && prob(affected_mob.satiety/10)) )
-			return
+	if(affected_mob.reagents.has_reagent("spaceacillin") || (affected_mob.satiety > 0 && prob(affected_mob.satiety/10)))
+		return
 
 	var/spread_range = 1
 
@@ -109,15 +114,9 @@
 	if(spread_flags & AIRBORNE)
 		spread_range++
 
-	if(!source)
-		if(affected_mob)
-			source = affected_mob
-		else
-			return
-
-	var/turf/T = source.loc
+	var/turf/T = affected_mob.loc
 	if(istype(T))
-		for(var/mob/living/carbon/C in oview(spread_range, source))
+		for(var/mob/living/carbon/C in oview(spread_range, affected_mob))
 			var/turf/V = get_turf(C)
 			if(V)
 				while(TRUE)
@@ -129,29 +128,6 @@
 						break
 					V = Temp
 
-/datum/disease/process()
-	if(!holder)
-		SSdisease.processing -= src
-		return
-
-	if(prob(infectivity))
-		spread(holder)
-
-	if(affected_mob)
-		for(var/datum/disease/D in affected_mob.viruses)
-			if(D != src)
-				if(IsSame(D))
-					qdel(D)
-
-		if(holder == affected_mob)
-			if(affected_mob.stat != DEAD)
-				stage_act()
-
-	if(!affected_mob)
-		if(prob(70))
-			if(--longevity<=0)
-				cure()
-
 
 /datum/disease/proc/cure()
 	if(affected_mob)
@@ -161,20 +137,6 @@
 		remove_virus()
 	qdel(src)
 
-
-/datum/disease/New()
-	if(required_organs && required_organs.len)
-		if(ishuman(affected_mob))
-			var/mob/living/carbon/human/H = affected_mob
-			for(var/obj/item/organ/O in required_organs)
-				if(!locate(O) in H.bodyparts)
-					if(!locate(O) in H.internal_organs)
-						cure()
-						return
-
-	SSdisease.processing += src
-
-
 /datum/disease/proc/IsSame(datum/disease/D)
 	if(istype(src, D.type))
 		return 1
@@ -191,11 +153,6 @@
 	return type
 
 
-/datum/disease/Destroy()
-	SSdisease.processing.Remove(src)
-	return ..()
-
-
 /datum/disease/proc/IsSpreadByTouch()
 	if(spread_flags & CONTACT_FEET || spread_flags & CONTACT_HANDS || spread_flags & CONTACT_GENERAL)
 		return 1

code/datums/diseases/advance/advance.dm

@@ -91,7 +91,7 @@
 	if(!(istype(D, /datum/disease/advance)))
 		return 0
 
-	if(src.GetDiseaseID() != D.GetDiseaseID())
+	if(GetDiseaseID() != D.GetDiseaseID())
 		return 0
 	return 1
 
@@ -116,7 +116,7 @@
 
 // Mix the symptoms of two diseases (the src and the argument)
 /datum/disease/advance/proc/Mix(datum/disease/advance/D)
-	if(!(src.IsSame(D)))
+	if(!(IsSame(D)))
 		var/list/possible_symptoms = shuffle(D.symptoms)
 		for(var/datum/symptom/S in possible_symptoms)
 			AddSymptom(new S.type)
@@ -156,7 +156,6 @@
 	return generated
 
 /datum/disease/advance/proc/Refresh(new_name = 0)
-	//to_chat(world, "[src.name] \ref[src] - REFRESH!")
 	GenerateProperties()
 	AssignProperties()
 	id = null
@@ -395,7 +394,7 @@
 		D.AssignName(new_name)
 		D.Refresh()
 
-		for(var/datum/disease/advance/AD in SSdisease.processing)
+		for(var/datum/disease/advance/AD in SSdisease.active_diseases)
 			AD.Refresh()
 
 		for(var/mob/living/carbon/human/H in shuffle(GLOB.living_mob_list))
@@ -410,13 +409,6 @@
 			name_symptoms += S.name
 		message_admins("[key_name_admin(user)] has triggered a custom virus outbreak of [D.name]! It has these symptoms: [english_list(name_symptoms)]")
 
-/*
-/mob/verb/test()
-
-	for(var/datum/disease/D in SSdisease.processing)
-		to_chat(src, "<a href='?_src_=vars;Vars=\ref[D]'>[D.name] - [D.holder]</a>")
-*/
-
 
 /datum/disease/advance/proc/totalStageSpeed()
 	return properties["stage_rate"]

code/datums/diseases/advance/symptoms/sneeze.dm

@@ -35,5 +35,5 @@ Bonus
 				M.emote("sniff")
 			else
 				M.emote("sneeze")
-				A.spread(A.holder, 5)
+				A.spread(5)
 	return

code/datums/diseases/advance/symptoms/symptoms.dm

@@ -18,7 +18,7 @@
 /datum/symptom/New()
 	var/list/S = SSdisease.list_symptoms
 	for(var/i = 1; i <= S.len; i++)
-		if(src.type == S[i])
+		if(type == S[i])
 			id = "[i]"
 			return
 	CRASH("We couldn't assign an ID!")

code/datums/diseases/appendicitis.dm

@@ -8,11 +8,11 @@
 	permeability_mod = 1
 	desc = "If left untreated the subject will become very weak, and may vomit often."
 	severity = "Dangerous!"
-	longevity = 1000
 	disease_flags = CAN_CARRY|CAN_RESIST
 	spread_flags = NON_CONTAGIOUS
 	visibility_flags = HIDDEN_PANDEMIC
 	required_organs = list(/obj/item/organ/appendix)
+	bypasses_immunity = TRUE // Immunity is based on not having an appendix; this isn't a virus
 
 /datum/disease/appendicitis/stage_act()
 	..()

code/datums/diseases/brainrot.dm

@@ -9,7 +9,7 @@
 	viable_mobtypes = list(/mob/living/carbon/human)
 	cure_chance = 15//higher chance to cure, since two reagents are required
 	desc = "This disease destroys the braincells, causing brain fever, brain necrosis and general intoxication."
-	required_organs = list(/obj/item/bodypart/head)
+	required_organs = list(/obj/item/organ/brain)
 	severity = DANGEROUS
 
 /datum/disease/brainrot/stage_act() //Removed toxloss because damaging diseases are pretty horrible. Last round it killed the entire station because the cure didn't work -- Urist -ACTUALLY Removed rather than commented out, I don't see it returning - RR

code/datums/diseases/dna_spread.dm

@@ -25,8 +25,8 @@
 		//Absorbs the target DNA.
 		strain_data["dna"] = new affected_mob.dna.type
 		affected_mob.dna.copy_dna(strain_data["dna"])
-		src.carrier = 1
-		src.stage = 4
+		carrier = TRUE
+		stage = 4
 		return
 
 	switch(stage)

code/datums/diseases/pierrot_throat.dm

@@ -10,7 +10,6 @@
 	permeability_mod = 0.75
 	desc = "If left untreated the subject will probably drive others to insanity."
 	severity = MEDIUM
-	longevity = 400
 
 /datum/disease/pierrot_throat/stage_act()
 	..()

code/datums/diseases/rhumba_beat.dm

@@ -13,7 +13,7 @@
 /datum/disease/rhumba_beat/stage_act()
 	..()
 	if(affected_mob.ckey == "rosham")
-		src.cure()
+		cure()
 		return
 	switch(stage)
 		if(2)

code/datums/diseases/transformation.dm

@@ -73,7 +73,6 @@
 	permeability_mod = 1
 	cure_chance = 1
 	disease_flags = CAN_CARRY|CAN_RESIST
-	longevity = 30
 	desc = "Monkeys with this disease will bite humans, causing humans to mutate into a monkey."
 	severity = BIOHAZARD
 	stage_prob = 4

code/datums/diseases/tuberculosis.dm

@@ -1,4 +1,5 @@
 /datum/disease/tuberculosis
+	form = "Disease"
 	name = "Fungal tuberculosis"
 	max_stages = 5
 	spread_text = "Airborne"
@@ -8,8 +9,9 @@
 	viable_mobtypes = list(/mob/living/carbon/human)
 	cure_chance = 5//like hell are you getting out of hell
 	desc = "A rare highly transmittable virulent virus. Few samples exist, rumoured to be carefully grown and cultured by clandestine bio-weapon specialists. Causes fever, blood vomiting, lung damage, weight loss, and fatigue."
-	required_organs = list(/obj/item/bodypart/head)
+	required_organs = list(/obj/item/organ/lungs)
 	severity = DANGEROUS
+	bypasses_immunity = TRUE // TB primarily impacts the lungs; it's also bacterial or fungal in nature; viral immunity should do nothing.
 
 /datum/disease/tuberculosis/stage_act() //it begins
 	..()

code/datums/mind.dm

@@ -629,10 +629,11 @@
 		text = "<i><b>[text]</b></i>: "
 		if (ishuman(current))
 			text += "<a href='?src=\ref[src];monkey=healthy'>healthy</a>|<a href='?src=\ref[src];monkey=infected'>infected</a>|<b>HUMAN</b>|other"
-		else if (ismonkey(current))
-			var/found = 0
-			for(var/datum/disease/D in current.viruses)
-				if(istype(D, /datum/disease/transformation/jungle_fever)) found = 1
+		else if(ismonkey(current))
+			var/found = FALSE
+			for(var/datum/disease/transformation/jungle_fever/JF in current.viruses)
+				found = TRUE
+				break
 
 			if(found)
 				text += "<a href='?src=\ref[src];monkey=healthy'>healthy</a>|<b>INFECTED</b>|<a href='?src=\ref[src];monkey=human'>human</a>|other"
@@ -1342,7 +1343,8 @@
 						src = M.mind
 						//to_chat(world, "DEBUG: \"healthy\": M=[M], M.mind=[M.mind], src=[src]!")
 					else if (istype(M) && length(M.viruses))
-						for(var/datum/disease/D in M.viruses)
+						for(var/thing in M.viruses)
+							var/datum/disease/D = thing
 							D.cure(0)
 			if("infected")
 				if (check_rights(R_ADMIN, 0))
@@ -1362,10 +1364,9 @@
 					var/mob/living/carbon/human/H = current
 					var/mob/living/carbon/monkey/M = current
 					if (istype(M))
-						for(var/datum/disease/D in M.viruses)
-							if (istype(D,/datum/disease/transformation/jungle_fever))
-								D.cure(0)
-								sleep(0) //because deleting of virus is doing throught spawn(0)
+						for(var/datum/disease/transformation/jungle_fever/JF in M.viruses)
+							JF.cure(0)
+							sleep(0) //because deleting of virus is doing throught spawn(0) //What
 						log_admin("[key_name(usr)] attempting to humanize [key_name(current)]")
 						message_admins("<span class='notice'>[key_name_admin(usr)] attempting to humanize [key_name_admin(current)]</span>")
 						H = M.humanize(TR_KEEPITEMS | TR_KEEPIMPLANTS | TR_KEEPORGANS | TR_KEEPDAMAGE | TR_KEEPVIRUS | TR_DEFAULTMSG)

code/game/data_huds.dm

@@ -62,7 +62,8 @@
 //called when a carbon changes virus
 /mob/living/carbon/proc/check_virus()
 	var/threat = 0
-	for(var/datum/disease/D in viruses)
+	for(var/thing in viruses)
+		var/datum/disease/D = thing
 		if(!(D.visibility_flags & HIDDEN_SCANNER))
 			if (D.severity != NONTHREAT) //a buffing virus gets an icon
 				threat = 2

code/game/gamemodes/changeling/powers/panacea.dm

@@ -41,6 +41,9 @@
 	user.reagents.add_reagent("antihol", 10)
 	user.reagents.add_reagent("mannitol", 25)
 
-	for(var/datum/disease/D in user.viruses)
+	for(var/thing in user.viruses)
+		var/datum/disease/D = thing
+		if(D.severity == NONTHREAT)
+			continue
 		D.cure()
 	return TRUE

code/game/gamemodes/miniantags/abduction/gland.dm

@@ -133,10 +133,9 @@
 	to_chat(owner, "<span class='warning'>You feel sick.</span>")
 	var/virus_type = pick(/datum/disease/beesease, /datum/disease/brainrot, /datum/disease/magnitis)
 	var/datum/disease/D = new virus_type()
-	D.carrier = 1
+	D.carrier = TRUE
 	owner.viruses += D
 	D.affected_mob = owner
-	D.holder = owner
 	owner.med_hud_set_status()
 
 

code/game/gamemodes/miniantags/monkey/monkey.dm

@@ -60,7 +60,6 @@
 
 		var/datum/disease/D = new /datum/disease/transformation/jungle_fever
 		D.visibility_flags = HIDDEN_SCANNER|HIDDEN_PANDEMIC
-		D.holder = carriermind.current
 		D.affected_mob = carriermind.current
 		carriermind.current.viruses += D
 	..()

code/game/machinery/cloning.dm

@@ -365,7 +365,7 @@
 			fl.forceMove(T)
 		unattached_flesh.Cut()
 		mess = FALSE
-		new /obj/effect/gibspawner/generic(loc)
+		new /obj/effect/gibspawner/generic(get_turf(src))
 		audible_message("<span class='italics'>You hear a splat.</span>")
 		icon_state = "pod_0"
 		return

code/game/objects/effects/decals/cleanable/aliens.dm

@@ -6,17 +6,10 @@
 	icon = 'icons/effects/blood.dmi'
 	icon_state = "xfloor1"
 	random_icon_states = list("xfloor1", "xfloor2", "xfloor3", "xfloor4", "xfloor5", "xfloor6", "xfloor7")
-	var/list/viruses = list()
 	blood_DNA = list("UNKNOWN DNA" = "X*")
 	bloodiness = MAX_SHOE_BLOODINESS
 	blood_state = BLOOD_STATE_XENO
 
-/obj/effect/decal/cleanable/xenoblood/Destroy()
-	for(var/datum/disease/D in viruses)
-		D.cure(0)
-	viruses = null
-	return ..()
-
 /obj/effect/decal/cleanable/xenoblood/xsplatter
 	random_icon_states = list("xgibbl1", "xgibbl2", "xgibbl3", "xgibbl4", "xgibbl5")
 
@@ -34,13 +27,9 @@
 	var/direction = pick(directions)
 	for(var/i = 0, i < pick(1, 200; 2, 150; 3, 50), i++)
 		sleep(2)
-		if (i > 0)
-			var/obj/effect/decal/cleanable/xenoblood/b = new /obj/effect/decal/cleanable/xenoblood/xsplatter(src.loc)
-			for(var/datum/disease/D in src.viruses)
-				var/datum/disease/ND = D.Copy(1)
-				b.viruses += ND
-				ND.holder = b
-		if (!step_to(src, get_step(src, direction), 0))
+		if(i > 0)
+			new /obj/effect/decal/cleanable/xenoblood/xsplatter(loc)
+		if(!step_to(src, get_step(src, direction), 0))
 			break
 
 /obj/effect/decal/cleanable/xenoblood/xgibs/ex_act()

code/game/objects/effects/decals/cleanable/humans.dm

@@ -4,17 +4,10 @@
 	icon = 'icons/effects/blood.dmi'
 	icon_state = "floor1"
 	random_icon_states = list("floor1", "floor2", "floor3", "floor4", "floor5", "floor6", "floor7")
-	var/list/viruses = list()
 	blood_DNA = list()
 	blood_state = BLOOD_STATE_HUMAN
 	bloodiness = MAX_SHOE_BLOODINESS
 
-/obj/effect/decal/cleanable/blood/Destroy()
-	for(var/datum/disease/D in viruses)
-		D.cure(0)
-	viruses = null
-	return ..()
-
 /obj/effect/decal/cleanable/blood/replace_decal(obj/effect/decal/cleanable/blood/C)
 	if (C.blood_DNA)
 		blood_DNA |= C.blood_DNA.Copy()
@@ -70,15 +63,11 @@
 /obj/effect/decal/cleanable/blood/gibs/proc/streak(list/directions)
 	set waitfor = 0
 	var/direction = pick(directions)
-	for (var/i = 0, i < pick(1, 200; 2, 150; 3, 50), i++)
+	for(var/i = 0, i < pick(1, 200; 2, 150; 3, 50), i++)
 		sleep(2)
-		if (i > 0)
-			var/obj/effect/decal/cleanable/blood/b = new /obj/effect/decal/cleanable/blood/splatter(src.loc)
-			for(var/datum/disease/D in src.viruses)
-				var/datum/disease/ND = D.Copy(1)
-				b.viruses += ND
-				ND.holder = b
-		if (!step_to(src, get_step(src, direction), 0))
+		if(i > 0)
+			new /obj/effect/decal/cleanable/blood/splatter(loc)
+		if(!step_to(src, get_step(src, direction), 0))
 			break
 
 /obj/effect/decal/cleanable/blood/gibs/up

code/game/objects/effects/decals/cleanable/misc.dm

@@ -80,9 +80,8 @@
 	icon = 'icons/effects/blood.dmi'
 	icon_state = "vomit_1"
 	random_icon_states = list("vomit_1", "vomit_2", "vomit_3", "vomit_4")
-	var/list/viruses = list()
 
-/obj/effect/decal/cleanable/vomit/attack_hand(var/mob/user)
+/obj/effect/decal/cleanable/vomit/attack_hand(mob/user)
 	if(ishuman(user))
 		var/mob/living/carbon/human/H = user
 		if(isflyperson(H))
@@ -98,12 +97,6 @@
 			reagents.trans_to(H, reagents.total_volume)
 			qdel(src)
 
-/obj/effect/decal/cleanable/vomit/Destroy()
-	for(var/datum/disease/D in viruses)
-		D.cure(0)
-	viruses = null
-	return ..()
-
 /obj/effect/decal/cleanable/vomit/old
 	name = "crusty dried vomit"
 	desc = "You try not to look at the chunks, and fail."

code/game/objects/effects/decals/cleanable/robots.dm

@@ -43,7 +43,6 @@
 	desc = "It's black and greasy. Looks like Beepsky made another mess."
 	icon = 'icons/mob/robots.dmi'
 	icon_state = "floor1"
-	var/viruses = list()
 	random_icon_states = list("floor1", "floor2", "floor3", "floor4", "floor5", "floor6", "floor7")
 	blood_state = BLOOD_STATE_OIL
 	bloodiness = MAX_SHOE_BLOODINESS
@@ -52,11 +51,5 @@
 	..()
 	reagents.add_reagent("oil", 30)
 
-/obj/effect/decal/cleanable/oil/Destroy()
-	for(var/datum/disease/D in viruses)
-		D.cure(0)
-	viruses = null
-	return ..()
-
 /obj/effect/decal/cleanable/oil/streak
 	random_icon_states = list("streak1", "streak2", "streak3", "streak4", "streak5")

code/game/objects/effects/spawners/gibspawner.dm

@@ -6,8 +6,8 @@
 	var/list/gibamounts = list() //amount to spawn for each gib decal type we'll spawn.
 	var/list/gibdirections = list() //of lists of possible directions to spread each gib decal type towards.
 
-/obj/effect/gibspawner/Initialize(mapload, list/viruses, datum/dna/MobDNA)
-	..()
+/obj/effect/gibspawner/Initialize(mapload, datum/dna/MobDNA)
+	. = ..()
 
 	if(gibtypes.len != gibamounts.len || gibamounts.len != gibdirections.len)
 		to_chat(world, "<span class='danger'>Gib list length mismatch!</span>")
@@ -29,13 +29,6 @@
 					var/mob/living/carbon/digester = loc
 					digester.stomach_contents += gib
 
-				if(viruses && viruses.len > 0)
-					for(var/datum/disease/D in viruses)
-						if(prob(virusProb))
-							var/datum/disease/viruus = D.Copy(1)
-							gib.viruses += viruus
-							viruus.holder = gib
-
 				if(MobDNA)
 					gib.blood_DNA[MobDNA.unique_enzymes] = MobDNA.blood_type
 				else if(istype(src, /obj/effect/gibspawner/generic)) // Probably a monkey
@@ -56,7 +49,7 @@
 /obj/effect/gibspawner/generic/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 40, 1)
 	gibdirections = list(list(WEST, NORTHWEST, SOUTHWEST, NORTH),list(EAST, NORTHEAST, SOUTHEAST, SOUTH), list())
-	..()
+	. = ..()
 
 /obj/effect/gibspawner/human
 	gibtypes = list(/obj/effect/decal/cleanable/blood/gibs/up,/obj/effect/decal/cleanable/blood/gibs/down,/obj/effect/decal/cleanable/blood/gibs,/obj/effect/decal/cleanable/blood/gibs,/obj/effect/decal/cleanable/blood/gibs/body,/obj/effect/decal/cleanable/blood/gibs/limb,/obj/effect/decal/cleanable/blood/gibs/core)
@@ -65,7 +58,7 @@
 /obj/effect/gibspawner/human/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 50, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST),list(WEST, NORTHWEST, SOUTHWEST),list(EAST, NORTHEAST, SOUTHEAST), GLOB.alldirs, GLOB.alldirs, list())
-	..()
+	. = ..()
 
 
 /obj/effect/gibspawner/humanbodypartless //only the gibs that don't look like actual full bodyparts (except torso).
@@ -75,7 +68,7 @@
 /obj/effect/gibspawner/humanbodypartless/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 50, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST),list(WEST, NORTHWEST, SOUTHWEST),list(EAST, NORTHEAST, SOUTHEAST), GLOB.alldirs, list())
-	..()
+	. = ..()
 
 
 /obj/effect/gibspawner/xeno
@@ -85,7 +78,7 @@
 /obj/effect/gibspawner/xeno/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 60, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST),list(WEST, NORTHWEST, SOUTHWEST),list(EAST, NORTHEAST, SOUTHEAST), GLOB.alldirs, GLOB.alldirs, list())
-	..()
+	. = ..()
 
 
 /obj/effect/gibspawner/xenobodypartless //only the gibs that don't look like actual full bodyparts (except torso).
@@ -96,7 +89,7 @@
 /obj/effect/gibspawner/xenobodypartless/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 60, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST),list(WEST, NORTHWEST, SOUTHWEST),list(EAST, NORTHEAST, SOUTHEAST), GLOB.alldirs, list())
-	..()
+	. = ..()
 
 /obj/effect/gibspawner/larva
 	gibtypes = list(/obj/effect/decal/cleanable/xenoblood/xgibs/larva, /obj/effect/decal/cleanable/xenoblood/xgibs/larva, /obj/effect/decal/cleanable/xenoblood/xgibs/larva/body, /obj/effect/decal/cleanable/xenoblood/xgibs/larva/body)
@@ -105,7 +98,7 @@
 /obj/effect/gibspawner/larva/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 60, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST), list(), GLOB.alldirs)
-	..()
+	. = ..()
 
 /obj/effect/gibspawner/larvabodypartless
 	gibtypes = list(/obj/effect/decal/cleanable/xenoblood/xgibs/larva, /obj/effect/decal/cleanable/xenoblood/xgibs/larva, /obj/effect/decal/cleanable/xenoblood/xgibs/larva)
@@ -114,7 +107,7 @@
 /obj/effect/gibspawner/larvabodypartless/Initialize()
 	playsound(src, 'sound/effects/blobattack.ogg', 60, 1)
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST), list())
-	..()
+	. = ..()
 
 /obj/effect/gibspawner/robot
 	sparks = 1
@@ -124,4 +117,4 @@
 /obj/effect/gibspawner/robot/Initialize()
 	gibdirections = list(list(NORTH, NORTHEAST, NORTHWEST),list(SOUTH, SOUTHEAST, SOUTHWEST),list(WEST, NORTHWEST, SOUTHWEST),list(EAST, NORTHEAST, SOUTHEAST), GLOB.alldirs, GLOB.alldirs)
 	gibamounts[6] = pick(0,1,2)
-	..()
+	. = ..()

code/game/objects/items/devices/scanners.dm

@@ -171,7 +171,8 @@ MASS SPECTROMETER
 		if(tdelta < (DEFIB_TIME_LIMIT * 10))
 			to_chat(user, "<span class='danger'>Subject died [tdelta / 10] seconds ago, defibrillation may be possible!</span>")
 
-	for(var/datum/disease/D in M.viruses)
+	for(var/thing in M.viruses)
+		var/datum/disease/D = thing
 		if(!(D.visibility_flags & HIDDEN_SCANNER))
 			to_chat(user, "<span class='alert'><b>Warning: [D.form] detected</b>\nName: [D.name].\nType: [D.spread_text].\nStage: [D.stage]/[D.max_stages].\nPossible Cure: [D.cure_text]</span>")
 

code/game/objects/items/weapons/melee/misc.dm

@@ -160,7 +160,7 @@
 		if (B && !QDELETED(B))
 			H.internal_organs -= B
 			qdel(B)
-		new /obj/effect/gibspawner/generic(H.loc, H.viruses, H.dna)
+		new /obj/effect/gibspawner/generic(get_turf(H), H.dna)
 		return (BRUTELOSS)
 
 /obj/item/weapon/melee/classic_baton/telescopic/attack_self(mob/user)

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

@@ -132,7 +132,7 @@
 					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))
@@ -142,11 +142,7 @@
 					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/shuttle_loan.dm.rej

@@ -0,0 +1,10 @@
+diff a/code/modules/events/shuttle_loan.dm b/code/modules/events/shuttle_loan.dm	(rejected hunks)
+@@ -21,7 +21,7 @@
+ 	var/thanks_msg = "The cargo shuttle should return in five minutes. Have some supply points for your trouble."
+ 
+ /datum/round_event/shuttle_loan/start()
+-	dispatch_type = ANTIDOTE_NEEDED /*pick(HIJACK_SYNDIE, RUSKY_PARTY, SPIDER_GIFT, DEPARTMENT_RESUPPLY, ANTIDOTE_NEEDED, PIZZA_DELIVERY) */
++	dispatch_type = pick(HIJACK_SYNDIE, RUSKY_PARTY, SPIDER_GIFT, DEPARTMENT_RESUPPLY, ANTIDOTE_NEEDED, PIZZA_DELIVERY)
+ 
+ /datum/round_event/shuttle_loan/announce()
+ 	SSshuttle.shuttle_loan = src

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

@@ -107,11 +107,13 @@
 
 /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)
 
@@ -124,11 +126,13 @@
 
 
 /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)
 
@@ -137,7 +141,8 @@
 		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

@@ -119,7 +119,8 @@
 				//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

@@ -222,6 +222,15 @@
 /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/carbon/life.dm.rej

@@ -0,0 +1,10 @@
+diff a/code/modules/mob/living/carbon/life.dm b/code/modules/mob/living/carbon/life.dm	(rejected hunks)
+@@ -12,7 +12,7 @@
+ 	if(..()) //not dead
+ 		handle_blood()
+ 
+-	if(stat != DEAD) // Reagent processing needs to be handled before breathing and such, to prevent edge cases
++	if(stat != DEAD)
+ 		handle_organs()
+ 
+ 	if(stat == DEAD)

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

@@ -19,14 +19,19 @@
 	var/datum/gas_mixture/environment = loc.return_air()
 
 	if(stat != DEAD)
-		//Breathing, if applicable
-		handle_breathing(times_fired)
+		//Chemicals in the body
+		handle_chemicals_in_body()
+
 	if(stat != DEAD)
 		//Mutations and radiation
 		handle_mutations_and_radiation()
+
 	if(stat != DEAD)
-		//Chemicals in the body
-		handle_chemicals_in_body()
+		//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()
@@ -66,6 +71,9 @@
 /mob/living/proc/handle_chemicals_in_body()
 	return
 
+/mob/living/proc/handle_diseases()
+	return
+
 /mob/living/proc/handle_diginvis()
 	if(!digitaldisguise)
 		src.digitaldisguise = image(loc = src)

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

@@ -0,0 +1,11 @@
+diff a/code/modules/mob/living/life.dm b/code/modules/mob/living/life.dm	(rejected hunks)
+@@ -64,9 +64,6 @@
+ /mob/living/proc/handle_diseases()
+ 	return
+ 
+-/mob/living/proc/handle_chemicals_in_body()
+-	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

@@ -372,7 +372,8 @@
 		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 \
@@ -423,7 +424,8 @@
 	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

@@ -149,7 +149,7 @@
 				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("eyes_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