things

and stuff...gonna need to get to those merge conflicts eventually. also
purged all mention of internal_organs by name from the face of the
earth. we have get_int_organ now...i may need to tweak shit. oh and i
broke some things...

code/modules/client/preferences.dm

@@ -1575,9 +1575,9 @@ datum/preferences
 					else
 						O.robotize()
 			else
-				var/obj/item/organ/internal/I = character.internal_organs_by_name[name]
+				var/obj/item/organ/internal/I = character.get_int_organ(name)
 				if(I)
-					if(status == "assisted")
+					if(status == "assisted")//add an actual organ for this?
 						I.mechassist()
 					else if(status == "mechanical")
 						I.robotize()

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

@@ -2,6 +2,7 @@
 	gender = MALE
 	hud_possible = list(HEALTH_HUD,STATUS_HUD,SPECIALROLE_HUD)
 	var/list/stomach_contents = list()
+	var/list/internal_organs	= list()
 	var/brain_op_stage = 0.0
 	var/list/datum/disease2/disease/virus2 = list()
 	var/antibodies = 0

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

@@ -256,8 +256,8 @@
 		else if(!client)
 			msg += "[t_He] [t_has] suddenly fallen asleep.\n"
 
-	if(!get_int_organ(/obj/item/organ/internal/brain))
-		msg += "<span class='deadsay'>It appears that it's brain is missing...</span>\n"
+	if(!src.get_int_organ(/obj/item/organ/internal/brain))
+		msg += "<span class='deadsay'>It appears that thier brain is missing...</span>\n"
 
 	var/list/wound_flavor_text = list()
 	var/list/is_destroyed = list()

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

@@ -1313,14 +1313,14 @@
 	..()
 
 /mob/living/carbon/human/proc/is_lung_ruptured()
-	var/obj/item/organ/internal/lungs/L = internal_organs_by_name["lungs"]
+	var/obj/item/organ/internal/lungs/L = get_int_organ(/obj/item/organ/internal/lungs)
 	if(!L)
 		return 0
 
 	return L.is_bruised()
 
 /mob/living/carbon/human/proc/rupture_lung()
-	var/obj/item/organ/internal/lungs/L = internal_organs_by_name["lungs"]
+	var/obj/item/organ/internal/lungs/L = get_int_organ(/obj/item/organ/internal/lungs)
 	if(!L)
 		return 0
 

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

@@ -18,7 +18,7 @@
 	if(((100 - total_burn) < config.health_threshold_dead) && stat == DEAD) //100 is the magic human max health number
 		ChangeToHusk()                                                      //BECAUSE NO ONE THOUGHT TO USE LIVING/VAR/MAXHEALTH I GUESS
 	if(species.can_revive_by_healing)
-		var/obj/item/organ/internal/brain/B = internal_organs_by_name["brain"]
+		var/obj/item/organ/internal/brain/B = get_int_organ(/obj/item/organ/internal/brain)
 		if(B)
 			if((health >= (config.health_threshold_dead / 100 * 75)) && stat == DEAD)
 				update_revive()
@@ -32,7 +32,7 @@
 		return 0	//godmode
 
 	if(species && species.has_organ["brain"])
-		var/obj/item/organ/internal/brain/sponge = internal_organs_by_name["brain"]
+		var/obj/item/organ/internal/brain/sponge = get_int_organ(/obj/item/organ/internal/brain)
 		if(sponge)
 			sponge.take_damage(amount, 1)
 			brainloss = sponge.damage
@@ -46,7 +46,7 @@
 		return 0	//godmode
 
 	if(species && species.has_organ["brain"])
-		var/obj/item/organ/internal/brain/sponge = internal_organs_by_name["brain"]
+		var/obj/item/organ/internal/brain/sponge = get_int_organ(/obj/item/organ/internal/brain)
 		if(sponge)
 			sponge.damage = min(max(amount, 0),(maxHealth*2))
 			brainloss = sponge.damage
@@ -60,7 +60,7 @@
 		return 0	//godmode
 
 	if(species && species.has_organ["brain"])
-		var/obj/item/organ/internal/brain/sponge = internal_organs_by_name["brain"]
+		var/obj/item/organ/internal/brain/sponge = get_int_organ(/obj/item/organ/internal/brain)
 		if(sponge)
 			brainloss = min(sponge.damage,maxHealth*2)
 		else

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

@@ -1,13 +1,13 @@
 /mob/living/carbon/human/proc/update_eyes()
-	var/obj/item/organ/internal/eyes/eyes = internal_organs_by_name["eyes"]
+	var/obj/item/organ/internal/eyes/eyes = get_int_organ(/obj/item/organ/internal/eyes)
 	if(eyes)
 		eyes.update_colour()
 		regenerate_icons()
 
-/mob/living/carbon/var/list/internal_organs = list()
+///mob/living/carbon/var/list/internal_organs = list()
 /mob/living/carbon/human/var/list/organs = list()
 /mob/living/carbon/human/var/list/organs_by_name = list() // map organ names to organs
-/mob/living/carbon/human/var/list/internal_organs_by_name = list() // so internal organs have less ickiness too
+//mob/living/carbon/human/var/list/internal_organs_by_name = list() // so internal organs have less ickiness too
 
 // Takes care of organ related updates, such as broken and missing limbs
 /mob/living/carbon/human/proc/handle_organs()
@@ -157,7 +157,7 @@ I use this to standardize shadowling dethrall code
 -- Crazylemon
 */
 /mob/living/carbon/human/proc/named_organ_parent(var/organ_name)
-	if (!(organ_name in internal_organs_by_name))
+	if (!get_int_organ(organ_name))
 		return null
-	var/obj/item/organ/O = internal_organs_by_name[organ_name]
+	var/obj/item/organ/internal/O = get_int_organ(organ_name)
 	return O.parent_organ

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

@@ -215,7 +215,7 @@ var/global/list/brutefireloss_overlays = list("1" = image("icon" = 'icons/mob/sc
 
 	if (radiation)
 
-		if((locate(src.internal_organs_by_name["resonant crystal"]) in src.internal_organs))
+		if(src.get_int_organ(/obj/item/organ/internal/nucleation/resonant_crystal))
 			var/rads = radiation/25
 			radiation -= rads
 			radiation -= 0.1
@@ -894,7 +894,7 @@ var/global/list/brutefireloss_overlays = list("1" = image("icon" = 'icons/mob/sc
 		//Vision //god knows why this is here
 		var/obj/item/organ/internal/vision
 		if(species.vision_organ)
-			vision = internal_organs_by_name[species.vision_organ]
+			vision = get_int_organ(/obj/item/organ/internal/eyes)//wot?
 
 		if(!species.vision_organ) // Presumably if a species has no vision organs, they see via some other means.
 			eye_blind =  0
@@ -1207,7 +1207,7 @@ var/global/list/brutefireloss_overlays = list("1" = image("icon" = 'icons/mob/sc
 /mob/living/carbon/human/proc/handle_heartbeat()
 	var/client/C = src.client
 	if(C && C.prefs.sound & SOUND_HEARTBEAT) //disable heartbeat by pref
-		var/obj/item/organ/internal/heart/H = internal_organs_by_name["heart"]
+		var/obj/item/organ/internal/heart/H = get_int_organ(/obj/item/organ/internal/heart)
 
 		if(!H) //H.status will runtime if there is no H (obviously)
 			return

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

@@ -47,14 +47,14 @@
 
 /datum/species/wryn/handle_death(var/mob/living/carbon/human/H)
 	for(var/mob/living/carbon/C in living_mob_list)
-		if(locate(/obj/item/organ/internal/wryn/hivenode) in C.internal_organs)
+		if(C.get_int_organ(/obj/item/organ/internal/wryn/hivenode))
 			C << "<span class='danger'><B>Your antennae tingle as you are overcome with pain...</B></span>"
 			C << "<span class='danger'>It feels like part of you has died.</span>"
 
 /datum/species/wryn/handle_attack_hand(var/mob/living/carbon/human/H, var/mob/living/carbon/human/M)
 	if(M.a_intent == I_HARM)
 		if(H.handcuffed)
-			if(!(locate(H.internal_organs_by_name["antennae"]) in H.internal_organs))	return
+			if(!H.get_int_organ(/obj/item/organ/internal/wryn/hivenode))	return
 			var/turf/p_loc = M.loc
 			var/turf/p_loc_m = H.loc
 
@@ -62,9 +62,10 @@
 			H << "<span class='danger'><B>[M] grips your antennae and starts violently pulling!<B></span>"
 			do_after(H, 250, target = src)
 			if(p_loc == M.loc && p_loc_m == H.loc)
-				qdel(H.internal_organs_by_name["antennae"])
+				var/obj/item/organ/internal/wryn/hivenode/node = new /obj/item/organ/internal/wryn/hivenode
 				H.remove_language("Wryn Hivemind")
-				new /obj/item/organ/internal/wryn/hivenode(M.loc)
+				node.remove(H)
+				node.loc = M.loc
 				M << "<span class='notice'>You hear a loud crunch as you mercilessly pull off [H]'s antennae.</span>"
 				H << "<span class='danger'><B>You hear a loud crunch as your antennae is ripped off your head by [M].</span></B>"
 				H << "<span class='danger'><span class='danger'><B>It's so quiet...</B></span>"

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

@@ -137,19 +137,17 @@
 		if((organ in H.organs))
 			qdel(organ)
 
-	for(var/obj/item/organ/internal/organ in H.contents)
-		if((organ in H.internal_organs))
-			qdel(organ)
+	//for(var/obj/item/organ/internal/organ in H.contents)
+	//	if((organ in H.internal_organs))
+	//		qdel(organ)
 
 	if(H.organs)                  H.organs.Cut()
-	if(H.internal_organs)         H.internal_organs.Cut()
+	//if(H.internal_organs)         H.internal_organs.Cut()
 	if(H.organs_by_name)          H.organs_by_name.Cut()
-	if(H.internal_organs_by_name) H.internal_organs_by_name.Cut()
 
 	H.organs = list()
 	H.internal_organs = list()
 	H.organs_by_name = list()
-	H.internal_organs_by_name = list()
 
 	for(var/limb_type in has_limbs)
 		var/list/organ_data = has_limbs[limb_type]
@@ -157,15 +155,12 @@
 		var/obj/item/organ/O = new limb_path(H)
 		organ_data["descriptor"] = O.name
 
-	for(var/organ in has_organ)
-		var/organ_type = has_organ[organ]
-		//world << "[organ_type]"//debug print
-		H.internal_organs_by_name[organ] = new organ_type(H,1)
-		H.internal_organs += new organ_type
+	for(var/index in has_organ)
+		var/organ = has_organ[index]
+		H.internal_organs += new organ(null)
 
 	for(var/obj/item/organ/internal/I in H.internal_organs)
-		if(!H.get_int_organ(I))
-			I.insert(src)
+		I.insert(H)
 
 	for(var/name in H.organs_by_name)
 		H.organs |= H.organs_by_name[name]
@@ -609,6 +604,7 @@
 Returns the path corresponding to the corresponding organ
 It'll return null if the organ doesn't correspond, so include null checks when using this!
 */
+//Fethas Todo:Do i need to redo this?
 /datum/species/proc/return_organ(var/organ_slot)
 	if(!(organ_slot in has_organ))
 		return null

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

@@ -502,7 +502,7 @@
 	reagent_tag = PROCESS_SYN
 
 	has_organ = list(
-		"brain" = /obj/item/organ/internal/mmi_holder/posibrain,
+		"brain" = /obj/item/organ/internal/brain/mmi_holder/posibrain,
 		"cell" = /obj/item/organ/internal/cell,
 		"optics" = /obj/item/organ/internal/optical_sensor
 		)

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

@@ -245,7 +245,7 @@ var/global/list/damage_icon_parts = list()
 		qdel(stand_icon)
 	stand_icon = new(species.icon_template ? species.icon_template : 'icons/mob/human.dmi',"blank")
 	var/icon_key = ""
-	var/obj/item/organ/internal/eyes/eyes = internal_organs_by_name["eyes"]
+	var/obj/item/organ/internal/eyes/eyes = get_int_organ(/obj/item/organ/internal/eyes)
 
 	if(eyes)
 		icon_key += "[rgb(eyes.eye_colour[1], eyes.eye_colour[2], eyes.eye_colour[3])]"

code/modules/power/apc.dm

@@ -652,7 +652,7 @@
 	//Synthetic human mob goes here.
 	if(istype(user,/mob/living/carbon/human))
 		var/mob/living/carbon/human/H = user
-		if(!isnull(H.internal_organs_by_name["cell"]) && H.a_intent == I_GRAB)
+		if(H.get_int_organ(/obj/item/organ/internal/cell) && H.a_intent == I_GRAB)
 			if(emagged || stat & BROKEN)
 				var/datum/effect/system/spark_spread/s = new /datum/effect/system/spark_spread
 				s.set_up(3, 1, src)

code/modules/power/supermatter/supermatter.dm

@@ -182,7 +182,7 @@
 			continue
 		// Where we're going, we don't need eyes.
 		// Prosthetic eyes will also protect against this business.
-		var/obj/item/organ/internal/eyes = l.internal_organs_by_name["eyes"]
+		var/obj/item/organ/internal/eyes/eyes = l.get_int_organ(/obj/item/organ/internal/eyes/)
 		if(!istype(eyes))
 			continue
 		l.hallucination = max(0, min(200, l.hallucination + power * config_hallucination_power * sqrt( 1 / max(1,get_dist(l, src)) ) ) )

code/modules/reagents/newchem/medicine.dm

@@ -525,7 +525,7 @@ datum/reagent/oculine/on_mob_life(var/mob/living/M as mob)
 	if(prob(80))
 		if(ishuman(M))
 			var/mob/living/carbon/human/H = M
-			var/obj/item/organ/internal/eyes/E = H.internal_organs_by_name["eyes"]
+			var/obj/item/organ/internal/eyes/E = H.get_int_organ(/obj/item/organ/internal/eyes)
 			if(istype(E))
 				E.damage = max(E.damage-1, 0)
 		M.eye_blurry = max(M.eye_blurry-1 , 0)

code/modules/reagents/oldchem/reagents/drink/reagents_alcohol.dm

@@ -63,8 +63,8 @@
 		M:drowsyness  = max(M:drowsyness, 30/sober_str)
 		if(ishuman(M))
 			var/mob/living/carbon/human/H = M
-			var/obj/item/organ/internal/liver/L = H.internal_organs_by_name["liver"]
-			if (istype(L))
+			if (H.get_int_organ(/obj/item/organ/internal/liver))
+				var/obj/item/organ/internal/liver/L = /obj/item/organ/internal/liver
 				L.take_damage(0.1, 1)
 			H.adjustToxLoss(0.1)
 	..()

code/modules/reagents/oldchem/reagents/reagents_admin.dm

@@ -24,7 +24,7 @@
 	M.eye_blind = 0
 	if(ishuman(M))
 		var/mob/living/carbon/human/H = M
-		var/obj/item/organ/internal/eyes/E = H.internal_organs_by_name["eyes"]
+		var/obj/item/organ/internal/eyes/E = H.get_int_organ(/obj/item/organ/internal/eyes)
 		if(istype(E))
 			E.damage = max(E.damage-5 , 0)
 	M.SetWeakened(0)

code/modules/reagents/oldchem/reagents/reagents_med.dm

@@ -78,8 +78,8 @@
 		var/mob/living/carbon/human/H = M
 
 		//Mitocholide is hard enough to get, it's probably fair to make this all internal organs
-		for(var/name in H.internal_organs_by_name)
-			var/obj/item/organ/internal/I = H.internal_organs_by_name[name]
+		for(var/name in H.internal_organs)
+			var/obj/item/organ/internal/I = H.get_int_organ(name)
 			if(I.damage > 0)
 				I.damage = max(I.damage-0.4, 0)
 	..()

code/modules/surgery/eye.dm

@@ -39,7 +39,7 @@
 		target.blinded += 1.5
 
 	fail_step(mob/living/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
-		var/obj/item/organ/internal/eyes/eyes = target.internal_organs_by_name["eyes"]
+		var/obj/item/organ/internal/eyes/eyes = target.get_int_organ(/obj/item/organ/internal/eyes)
 		var/obj/item/organ/external/affected = target.get_organ(target_zone)
 		user.visible_message("\red [user]'s hand slips, slicing [target]'s eyes wth \the [tool]!" , \
 		"\red Your hand slips, slicing [target]'s eyes wth \the [tool]!" )

code/modules/surgery/organs/augments_eyes.dm

@@ -7,13 +7,12 @@
 	parent_organ = "eyes"
 	w_class = 1
 
-	var/sight_flags = 0
+	var/vision_flags = 0
 	var/list/eye_colour = list(0,0,0)
 	var/list/old_eye_colour = list(0,0,0)
 	var/flash_protect = 0
 	var/aug_message = "Your vision is augmented!"
 
-
 /obj/item/organ/internal/cyberimp/eyes/proc/update_colour()
 	if(!owner)
 		return
@@ -38,11 +37,12 @@
 		HMN.update_eyes()
 	if(aug_message && !special)
 		owner << "<span class='notice'>[aug_message]</span>"
-	M.sight |= sight_flags
+	M.sight |= vision_flags
+	world << "[M.sight]"
 
 /obj/item/organ/internal/cyberimp/eyes/remove(var/mob/living/carbon/M, var/special = 0)
 	..()
-	M.sight ^= sight_flags
+	M.sight ^= vision_flags
 	if(istype(owner,/mob/living/carbon/human) && eye_colour)
 		var/mob/living/carbon/human/HMN = owner
 		HMN.r_eyes = old_eye_colour[1]
@@ -52,7 +52,7 @@
 
 /obj/item/organ/internal/cyberimp/eyes/on_life()
 	..()
-	owner.sight |= sight_flags
+	owner.sight |= vision_flags
 
 /obj/item/organ/internal/cyberimp/eyes/emp_act(severity)
 	if(!owner)
@@ -77,14 +77,14 @@
 	eye_colour = rgb(0, 0, 0)
 	implant_color = "#000000"
 	origin_tech = "materials=6;programming=4;biotech=6;magnets=5"
-	sight_flags = SEE_MOBS | SEE_OBJS | SEE_TURFS
+	vision_flags = SEE_MOBS | SEE_OBJS | SEE_TURFS
 
 /obj/item/organ/internal/cyberimp/eyes/thermals
 	name = "Thermals implant"
 	desc = "These cybernetic eye implants will give you Thermal vision. Vertical slit pupil included."
 	eye_colour = rgb(255, 204, 0)
 	implant_color = "#FFCC00"
-	sight_flags = SEE_MOBS
+	vision_flags = SEE_MOBS
 	flash_protect = -1
 	origin_tech = "materials=6;programming=4;biotech=5;magnets=5;syndicate=4"
 	aug_message = "You see prey everywhere you look..."
@@ -137,5 +137,6 @@
 	implant_color = "#101010"
 	flash_protect = 2
 	// Welding with thermals will still hurt your eyes a bit.
+
 /obj/item/organ/internal/cyberimp/eyes/shield/emp_act(severity)
 	return

code/modules/surgery/organs/augments_internal.dm

@@ -8,6 +8,8 @@
 	status = ORGAN_ROBOT
 	var/implant_color = "#FFFFFF"
 	var/implant_overlay
+	tough = 1 //not easyly broken by combat damage
+	sterile = 1 //not very germy
 
 /obj/item/organ/internal/cyberimp/New(var/mob/M = null)
 	if(iscarbon(M))

code/modules/surgery/organs/blood.dm

@@ -87,7 +87,7 @@ var/const/BLOOD_VOLUME_SURVIVE = 122
 
 		// Damaged heart virtually reduces the blood volume, as the blood isn't
 		// being pumped properly anymore.
-		var/obj/item/organ/internal/heart/heart = internal_organs_by_name["heart"]
+		var/obj/item/organ/internal/heart/heart = get_int_organ(/obj/item/organ/internal/heart)
 
 		if(heart)
 			if(heart.damage > 1 && heart.damage < heart.min_bruised_damage)

code/modules/surgery/organs/organ.dm

@@ -32,19 +32,20 @@ var/list/organ_cache = list()
 /obj/item/organ/Destroy()
 	if(!owner)
 		return ..()
-/*
+
 
 	if(istype(owner, /mob/living/carbon))
 		if((owner.internal_organs) && (src in owner.internal_organs))
-			owner.internal_organs -= src
+			var/obj/item/organ/internal/O = src
+			O.remove(owner)
 		if(istype(owner, /mob/living/carbon/human))
-			if((owner.internal_organs_by_name) && (src in owner.internal_organs_by_name))
-				owner.internal_organs_by_name -= src
-			if((owner.organs) && (src in owner.organs))
-				owner.organs -= src
-			if((owner.organs_by_name) && (src in owner.organs_by_name))
-				owner.organs_by_name -= src
-*/
+			var/obj/item/organ/internal/O = src
+			O.remove(owner)
+		if((owner.organs) && (src in owner.organs))
+			owner.organs -= src
+		if((owner.organs_by_name) && (src in owner.organs_by_name))
+			owner.organs_by_name -= src
+
 	if(src in owner.contents)
 		owner.contents -= src
 
@@ -101,8 +102,8 @@ var/list/organ_cache = list()
 		owner.death()
 
 /obj/item/organ/process()
-	if(loc != owner)
-		owner = null
+	//if(loc != owner)
+	//	owner = null
 
 	//dead already, no need for more processing
 	if(status & ORGAN_DEAD)
@@ -289,10 +290,10 @@ var/list/organ_cache = list()
 	if(!istype(owner))
 		return
 
-	if(is_primary_organ())
-		owner.internal_organs_by_name[organ_tag] = null
-		owner.internal_organs_by_name -= organ_tag
-		owner.internal_organs_by_name -= null // uh what does this line even do this seems silly
+	//if(is_primary_organ())//Toddo from fethas:Do i need to move ths?
+	//	owner.internal_organs_by_name[organ_tag] = null
+	//	owner.internal_organs_by_name -= organ_tag
+	//	owner.internal_organs_by_name -= null // uh what does this line even do this seems silly
 
 	owner.internal_organs -= src
 
@@ -320,10 +321,9 @@ var/list/organ_cache = list()
 
 	owner = target
 	processing_objects -= src
-	target.internal_organs |= src
 	affected.internal_organs |= src
-	if (!(organ_tag in target.internal_organs_by_name))
-		target.internal_organs_by_name[organ_tag] = src // In case multiple of the same type are inserted, only the first one is the primary organ
+	if (!target.get_int_organ(src))
+		target.internal_organs |= src
 	src.loc = target
 	if(robotic)
 		status |= ORGAN_ROBOT
@@ -342,4 +342,4 @@ I use this so that this can be made better once the organ overhaul rolls out --
 		O = owner
 	if (!istype(owner)) // You're not the primary organ of ANYTHING, bucko
 		return 0
-	return src == O.internal_organs_by_name[organ_tag]
+	return src == O.get_int_organ(organ_tag)

code/modules/surgery/organs/organ_external.dm

@@ -71,7 +71,9 @@
 
 	if(internal_organs)
 		for(var/obj/item/organ/internal/O in internal_organs)
-			qdel(O)
+			internal_organs -= O
+			O.remove(owner)
+			//qdel(O)
 
 	return ..()
 
@@ -95,11 +97,12 @@
 				if(contents.len)
 					var/obj/item/removing = pick(contents)
 					removing.loc = get_turf(user.loc)
-					var/obj/item/organ/O = removing
+					var/obj/item/organ/internal/O = removing
 					if(istype(O))
 						O.status |= ORGAN_CUT_AWAY
-						spread_germs_to_organ(O,user) // This wouldn't be any cleaner than the actual surgery
-						O.removed(user)
+						if(!O.sterile)
+							spread_germs_to_organ(O,user) // This wouldn't be any cleaner than the actual surgery
+						O.remove(src)
 					if(!(user.l_hand && user.r_hand))
 						user.put_in_hands(removing)
 					user.visible_message("<span class='danger'><b>[user]</b> extracts [removing] from [src] with [W]!")
@@ -166,7 +169,8 @@
 		// Damage an internal organ
 		if(internal_organs && internal_organs.len)
 			var/obj/item/organ/internal/I = pick(internal_organs)
-			I.take_damage(brute / 2)
+			if(!I.tough)//mostly for cybernetic organs
+				I.take_damage(brute / 2)
 			brute -= brute / 2
 
 	if(status & ORGAN_BROKEN && prob(40) && brute)

code/modules/surgery/organs/organ_icon.dm

@@ -33,7 +33,7 @@ var/global/list/limb_icon_cache = list()
 
 /obj/item/organ/external/head/sync_colour_to_human(var/mob/living/carbon/human/human)
 	..()
-	var/obj/item/organ/internal/eyes/eyes = owner.get_int_organ("eyes")//owner.internal_organs_by_name["eyes"]
+	var/obj/item/organ/internal/eyes/eyes = owner.get_int_organ(/obj/item/organ/internal/eyes)//owner.internal_organs_by_name["eyes"]
 	if(eyes) eyes.update_colour()
 
 /obj/item/organ/external/head/removed()
@@ -48,7 +48,7 @@ var/global/list/limb_icon_cache = list()
 		return
 
 	if(species.has_organ["eyes"])
-		var/obj/item/organ/internal/eyes/eyes = owner.internal_organs_by_name["eyes"]
+		var/obj/item/organ/internal/eyes/eyes = owner.get_int_organ(/obj/item/organ/internal/eyes)//owner.internal_organs_by_name["eyes"]
 		if(species.eyes)
 			var/icon/eyes_icon = new/icon('icons/mob/human_face.dmi', species.eyes)
 			if(eyes)

code/modules/surgery/organs/organ_internal.dm

@@ -9,6 +9,8 @@
 	var/slot
 	vital = 0
 	var/organ_action_name = null
+	var/sterile = 0 //can the organ be infected by germs?
+	var/tough = 0 //can organ be easily damaged?
 
 /obj/item/organ/internal/proc/insert(mob/living/carbon/M, special = 0)
 	if(!iscarbon(M) || owner == M)
@@ -19,7 +21,9 @@
 		replaced.remove(M, special = 1)
 
 	owner = M
+
 	M.internal_organs |= src
+	//M.internal_organs_by_name[src] |= src(H,1)
 	loc = null
 	if(organ_action_name)
 		action_button_name = organ_action_name
@@ -29,6 +33,7 @@
 	owner = null
 	if(M)
 		M.internal_organs -= src
+		//M.internal_organs_by_name[src] -= src
 		if(vital && !special)
 			M.death()
 
@@ -192,6 +197,16 @@
 		owner.b_eyes ? owner.b_eyes : 0
 		)
 
+/obj/item/organ/internal/eyes/insert(mob/living/carbon/M, special = 0)
+// Apply our eye colour to the target.
+	if(istype(M) && eye_colour)
+		var/mob/living/carbon/human/eyes = M
+		eyes.r_eyes = eye_colour[1]
+		eyes.g_eyes = eye_colour[2]
+		eyes.b_eyes = eye_colour[3]
+		eyes.update_eyes()
+	..()
+
 /obj/item/organ/internal/eyes/surgeryize()
 	if(!owner)
 		return
@@ -200,6 +215,7 @@
 	owner.eye_blurry = 0
 	owner.eye_blind = 0
 
+
 /obj/item/organ/internal/liver
 	name = "liver"
 	icon_state = "liver"
@@ -282,7 +298,7 @@
 			name = "inflamed appendix"
 	..()
 */
-
+//shadowling tumor
 /obj/item/organ/internal/shadowtumor
 	name = "black tumor"
 	desc = "A tiny black mass with red tendrils trailing from it. It seems to shrivel in the light."
@@ -305,10 +321,34 @@
 	if(isturf(loc))
 		var/turf/T = loc
 		var/light_count = T.get_lumcount()
+		world << "[light_count]"
 		if(light_count > 4 && health > 0) //Die in the light
 			health--
 		else if(light_count < 2 && health < 3) //Heal in the dark
 			health++
 		if(health <= 0)
 			visible_message("<span class='warning'>[src] collapses in on itself!</span>")
-			qdel(src)
+			qdel(src)
+
+//debug and adminbus....
+
+/obj/item/organ/internal/honktumor
+	name = "banana tumor"
+	desc = "A tiny yellow mass shaped like..a banana?"
+	icon_state = "honktumor"
+	origin_tech = "biotech=1"
+	w_class = 1
+	parent_organ = "head"
+	slot = "brain_tumor"
+	health = 3
+
+/obj/item/organ/internal/honktumor/insert(mob/living/carbon/M, special = 0)
+
+		M.mutations.Add(CLUMSY)
+		M.dna.SetSEState(COMICBLOCK,1,1)
+		//genemutcheck(H,COMICBLOCK,null,MUTCHK_FORCED)
+
+/obj/item/organ/internal/honktumor/remove(mob/living/carbon/M, special = 0)
+		M.mutations.Remove(CLUMSY)
+		M.mutations.Remove(COMICBLOCK)
+		//genemutcheck(H,COMICBLOCK,null,MUTCHK_FORCED)

code/modules/surgery/organs/subtypes/machine.dm

@@ -88,7 +88,7 @@
 	..()
 
 // Used for an MMI or posibrain being installed into a human.
-/obj/item/organ/internal/mmi_holder
+/obj/item/organ/internal/brain/mmi_holder
 	name = "brain"
 	organ_tag = "brain"
 	parent_organ = "chest"
@@ -97,7 +97,7 @@
 	slot = "brain"
 	var/obj/item/device/mmi/stored_mmi
 
-/obj/item/organ/internal/mmi_holder/proc/update_from_mmi()
+/obj/item/organ/internal/brain/mmi_holder/proc/update_from_mmi()
 	if(!stored_mmi)
 		return
 	name = stored_mmi.name
@@ -105,7 +105,7 @@
 	icon = stored_mmi.icon
 	icon_state = stored_mmi.icon_state
 
-/obj/item/organ/internal/mmi_holder/remove(var/mob/living/user)
+/obj/item/organ/internal/brain/mmi_holder/remove(var/mob/living/user)
 	if(stored_mmi)
 		stored_mmi.loc = get_turf(src)
 		if(owner.mind)
@@ -117,7 +117,7 @@
 		holder_mob.unEquip(src)
 	qdel(src)
 
-/obj/item/organ/internal/mmi_holder/New()
+/obj/item/organ/internal/brain/mmi_holder/New()
 	..()
 	// This is very ghetto way of rebooting an IPC. TODO better way.
 	spawn(1)
@@ -125,7 +125,7 @@
 			owner.stat = CONSCIOUS
 			owner.visible_message("<span class='danger'>\The [owner] twitches visibly!</span>")
 
-/obj/item/organ/internal/mmi_holder/posibrain/New()
+/obj/item/organ/internal/brain/mmi_holder/posibrain/New()
 	robotize()
 	stored_mmi = new /obj/item/device/mmi/posibrain(src)
 	..()

code/modules/surgery/organs/subtypes/xenos.dm

@@ -2,6 +2,8 @@
 	origin_tech = "biotech=5"
 	icon_state = "xgibmid2"
 	var/list/alien_powers = list()
+	tough = 1
+	sterile = 1
 
 /obj/item/organ/internal/xenos/New()
 	for(var/A in alien_powers)

code/modules/surgery/organs_internal.dm

@@ -163,7 +163,8 @@
 		for(var/obj/item/organ/internal/I in affected.internal_organs)
 			if(I && I.damage > 0)
 				if(I.robotic < 2)
-					spread_germs_to_organ(I, user)
+					if(!I.sterile)
+						spread_germs_to_organ(I, user)
 					user.visible_message("[user] starts treating damage to [target]'s [I.name] with [tool_name].", \
 					"You start treating damage to [target]'s [I.name] with [tool_name]." )
 
@@ -370,13 +371,13 @@
 
 		if(O.organ_tag == "limb")
 			return 0
-		else if(target.species.has_organ[O.organ_tag])
+		else if(target.species.has_organ[O.organ_tag])//need to change this around for cybernetic implants
 
 			if(O.damage > (O.max_damage * 0.75))
 				user << "\red \The [O.organ_tag] [o_is] in no state to be transplanted."
 				return 2
 
-			if(!target.internal_organs_by_name[O.organ_tag])
+			if(!target.get_int_organ(O))
 				organ_missing = 1
 			else
 				user << "\red \The [target] already has [o_a][O.organ_tag]."

code/modules/surgery/robotics.dm

@@ -319,7 +319,7 @@
 		user.visible_message("\blue [user] has decoupled [target]'s [target.op_stage.current_organ] with \the [tool]." , \
 		"\blue You have decoupled [target]'s [target.op_stage.current_organ] with \the [tool].")
 
-		var/obj/item/organ/internal/I = target.internal_organs_by_name[target.op_stage.current_organ]
+		var/obj/item/organ/internal/I = target.get_int_organ(target.op_stage.current_organ)
 		if(I && istype(I))
 			I.status |= ORGAN_CUT_AWAY
 
@@ -369,7 +369,7 @@
 		user.visible_message("\blue [user] has reattached [target]'s [target.op_stage.current_organ] with \the [tool]." , \
 		"\blue You have reattached [target]'s [target.op_stage.current_organ] with \the [tool].")
 
-		var/obj/item/organ/internal/I = target.internal_organs_by_name[target.op_stage.current_organ]
+		var/obj/item/organ/internal/I = target.get_int_organ(target.op_stage.current_organ)
 		if(I && istype(I))
 			I.status &= ~ORGAN_CUT_AWAY
 
@@ -414,7 +414,7 @@
 			user << "<span class='danger'>You're pretty sure [target.species.name_plural] don't normally have a brain.</span>"
 			return 2
 
-		if(!isnull(target.internal_organs["brain"]))
+		if(target.get_int_organ(/obj/item/organ/internal/brain/))
 			user << "<span class='danger'>Your subject already has a brain.</span>"
 			return 2
 
@@ -432,11 +432,11 @@
 		"\blue You have installed \the [tool] into [target]'s [affected.name].")
 
 		var/obj/item/device/mmi/M = tool
-		var/obj/item/organ/internal/mmi_holder/holder = new(target, 1)
+		var/obj/item/organ/internal/brain/mmi_holder/holder = new()
 		if (istype(M, /obj/item/device/mmi/posibrain))
 			holder.robotize()
 
-		target.internal_organs_by_name["brain"] = holder
+		holder.insert(target)
 		user.unEquip(tool)
 		tool.forceMove(holder)
 		holder.stored_mmi = tool

code/modules/surgery/surgery.dm

@@ -68,7 +68,7 @@
 
 /proc/spread_germs_to_organ(obj/item/organ/E, mob/living/carbon/human/user)
 	if(!istype(user) || !istype(E)) return
-
+	//world << "Germ spread: [E] : [E.owner]"
 	var/germ_level = user.germ_level
 	if(user.gloves)
 		germ_level = user.gloves.germ_level

code/modules/virus2/effect.dm

@@ -221,7 +221,7 @@
 	activate(var/mob/living/carbon/mob,var/multiplier)
 		if(istype(mob, /mob/living/carbon/human))
 			var/mob/living/carbon/human/H = mob
-			var/obj/item/organ/internal/brain/B = H.internal_organs_by_name["brain"]
+			var/obj/item/organ/internal/brain/B = H.get_int_organ(/obj/item/organ/internal/brain)
 			if (B.damage < B.min_broken_damage)
 				B.take_damage(5, 1)
 		else
@@ -442,7 +442,7 @@
 	activate(var/mob/living/carbon/mob,var/multiplier)
 		if(istype(mob, /mob/living/carbon/human))
 			var/mob/living/carbon/human/H = mob
-			var/obj/item/organ/internal/brain/B = H.internal_organs_by_name["brain"]
+			var/obj/item/organ/internal/brain/B = H.get_int_organ(/obj/item/organ/internal/brain)
 			if (B.damage < B.min_broken_damage)
 				B.take_damage(1, 1)
 		else
@@ -704,7 +704,7 @@ var/list/compatible_mobs = list(/mob/living/carbon/human)
 	activate(var/mob/living/carbon/mob,var/multiplier)
 		if(istype(mob, /mob/living/carbon/human))
 			var/mob/living/carbon/human/H = mob
-			var/obj/item/organ/internal/brain/B = H.internal_organs_by_name["brain"]
+			var/obj/item/organ/internal/brain/B = H.get_int_organ(/obj/item/organ/internal/brain)
 			if (B.damage < B.min_broken_damage)
 				B.take_damage(0.5, 1)
 		else
@@ -936,7 +936,7 @@ var/list/compatible_mobs = list(/mob/living/carbon/human)
 	name = "Watery Eyes"
 	stage = 1
 	activate(var/mob/living/carbon/human/mob,var/multiplier)
-		var/obj/item/organ/internal/eyes/E = mob.internal_organs_by_name["eyes"]
+		var/obj/item/organ/internal/eyes/E = mob.get_int_organ(/obj/item/organ/internal/eyes)
 		if(!istype(E) || (E.status & ORGAN_ROBOT)) // No eyes or robotic eyes? No problem!
 			return
 		mob << "<span class='warning'>Your eyes sting and water!</span>"