Merge branch 'master' of https://github.com/ParadiseSS13/Paradise into mitocholide_organ_rejuv

code/modules/admin/admin.dm

@@ -139,6 +139,9 @@ var/global/nologevent = 0
 			else
 				body += "<A href='?_src_=holder;makeanimal=\ref[M]'>Animalize</A> | "
 
+			if(istype(M, /mob/dead/observer))
+				body += "<a href='?_src_=holder;incarn_ghost=\ref[M]'>Re-incarnate</a> | "
+
 			// DNA2 - Admin Hax
 			if(M.dna && iscarbon(M))
 				body += "<br><br>"

code/modules/admin/topic.dm

@@ -1523,6 +1523,14 @@
 
 		usr.client.cmd_admin_animalize(M)
 
+	else if(href_list["incarn_ghost"])
+		if(!check_rights(R_SPAWN)) return
+
+		var/mob/dead/observer/G = locate(href_list["incarn_ghost"])
+		if(!istype(G))
+			usr << "This will only work on /mob/dead/observer"
+		G.incarnate_ghost()
+
 	else if(href_list["togmutate"])
 		if(!check_rights(R_SPAWN))	return
 

code/modules/client/preferences.dm

@@ -1585,8 +1585,6 @@ var/global/list/special_role_times = list( //minimum age (in days) for accounts
 
 	character.real_name = real_name
 	character.name = character.real_name
-	if(character.dna)
-		character.dna.real_name = character.real_name
 
 	character.flavor_text = flavor_text
 	character.med_record = med_record
@@ -1696,6 +1694,9 @@ var/global/list/special_role_times = list( //minimum age (in days) for accounts
 			message_admins("[key_name_admin(character)] has spawned with their gender as plural or neuter. Please notify coders.")
 			character.change_gender(MALE)
 
+	character.dna.ready_dna(character)
+	character.sync_organ_dna(assimilate=1)
+
 /datum/preferences/proc/open_load_dialog(mob/user)
 
 	var/DBQuery/query = dbcon.NewQuery("SELECT slot,real_name FROM [format_table_name("characters")] WHERE ckey='[user.ckey]' ORDER BY slot")

code/modules/mob/dead/observer/observer.dm

@@ -636,3 +636,13 @@ This is the proc mobs get to turn into a ghost. Forked from ghostize due to comp
 		return 0
 	usr.visible_message("<span class='deadsay'><b>[src]</b> points to [A].</span>")
 	return 1
+
+/mob/dead/observer/proc/incarnate_ghost()
+	if(!client)
+		return
+	var/mob/living/carbon/human/new_char = new(get_turf(src))
+	client.prefs.copy_to(new_char)
+	if(mind)
+		mind.transfer_to(new_char)
+	else
+		new_char.key = key

code/modules/mob/holder.dm

@@ -34,6 +34,14 @@
 	for(var/mob/living/M in contents)
 		M.show_message(message,m_type)
 
+/obj/item/weapon/holder/emp_act(var/intensity)
+	for(var/mob/living/M in contents)
+		M.emp_act(intensity)
+
+/obj/item/weapon/holder/ex_act(var/intensity)
+	for(var/mob/living/M in contents)
+		M.ex_act(intensity)
+
 /obj/item/weapon/holder/container_resist(var/mob/living/L)
 	var/mob/M = src.loc                      //Get our mob holder (if any).
 
@@ -91,4 +99,5 @@
 /obj/item/weapon/holder/mouse
 	name = "mouse"
 	desc = "It's a small, disease-ridden rodent."
+	icon = 'icons/mob/animal.dmi'
 	icon_state = "mouse_gray"

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

@@ -30,9 +30,6 @@
 			user << "<span class='userdanger'>Somehow, this MMI still has a brain in it. Report this to the bug tracker.</span>"
 			log_to_dd("[user] tried to stick a [O] into [src] in [get_area(src)], but the held brain variable wasn't cleared")
 			return
-		if(B.status & ORGAN_DEAD) // As it stood, a brain would never become unviable for MMI usage. Perhaps we should keep it that way?
-			user << "<span class='warning'>This [B] is dead</span>"
-			return
 		for(var/mob/V in viewers(src, null))
 			V.show_message("<span class='notice'>[user] sticks \a [O] into \the [src].</span>")
 		brainmob = B.brainmob

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

@@ -59,6 +59,8 @@
 
 /obj/item/organ/internal/brain/remove(var/mob/living/user,special = 0)
 
+	name = "[dna.real_name]'s [initial(name)]"
+
 	if(!owner) return ..() // Probably a redundant removal; just bail
 
 	var/obj/item/organ/internal/brain/B = src
@@ -77,7 +79,7 @@
 
 /obj/item/organ/internal/brain/insert(var/mob/living/target,special = 0)
 
-	name = "brain"
+	name = "[initial(name)]"
 	var/brain_already_exists = 0
 	if(istype(target,/mob/living/carbon/human)) // No more IPC multibrain shenanigans
 		if(target.get_int_organ(/obj/item/organ/internal/brain))

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

@@ -147,11 +147,14 @@
 /*
 When assimilate is 1, organs that have a different UE will still have their DNA overriden by that of the host
 Otherwise, this restricts itself to organs that share the UE of the host.
+
+old_ue: Set this to a UE string, and this proc will overwrite the dna of organs that have that UE, instead of the host's present UE
 */
-/mob/living/carbon/human/proc/sync_organ_dna(var/assimilate = 1)
+/mob/living/carbon/human/proc/sync_organ_dna(var/assimilate = 1, var/old_ue = null)
+	var/ue_to_compare = (old_ue) ? old_ue : dna.unique_enzymes
 	var/list/all_bits = internal_organs|organs
 	for(var/obj/item/organ/O in all_bits)
-		if(assimilate || O.dna.unique_enzymes == dna.unique_enzymes)
+		if(assimilate || O.dna.unique_enzymes == ue_to_compare)
 			O.set_dna(dna)
 
 /*

code/modules/mob/living/living.dm

@@ -385,7 +385,6 @@
 		var/mob/living/carbon/C = src
 		C.handcuffed = initial(C.handcuffed)
 		C.heart_attack = 0
-		C.brain_op_stage = 0
 
 		// restore all of the human's blood and reset their shock stage
 		if(ishuman(src))

code/modules/surgery/limb_reattach.dm

@@ -151,7 +151,7 @@
 	return 1
 
 /datum/surgery_step/limb/connect/fail_step(mob/living/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
-	var/obj/item/organ/external/E = tool
+	var/obj/item/organ/external/E = target.get_organ(target_zone)
 	user.visible_message("<span class='alert'>[user]'s hand slips, damaging [target]'s [E.amputation_point]!</span>", \
 	"<span class='alert'>Your hand slips, damaging [target]'s [E.amputation_point]!</span>")
 	target.apply_damage(10, BRUTE, null, sharp=1)

code/modules/surgery/organs/organ.dm

@@ -84,7 +84,7 @@ var/list/organ_cache = list()
 		return
 
 	//Process infections
-	if ((status & ORGAN_ROBOT) || (sterile) ||(owner && owner.species && (owner.species.flags & IS_PLANT)))
+	if ((status & ORGAN_ROBOT) || sterile ||(owner && owner.species && (owner.species.flags & IS_PLANT)))
 		germ_level = 0
 		return
 

code/modules/surgery/organs/organ_external.dm

@@ -30,8 +30,9 @@
 	var/cannot_amputate
 	var/cannot_break
 	var/s_tone
-	var/list/s_col = list()
+	var/list/s_col = null // If this is instantiated, it should be a list of length 3
 	var/list/wounds = list()
+	var/list/child_icons = list()
 	var/number_wounds = 0 // cache the number of wounds, which is NOT wounds.len!
 	var/perma_injury = 0
 	// 0: Don't fail when at full damage
@@ -64,6 +65,7 @@
 	var/amputation_point // Descriptive string used in amputation.
 	var/can_grasp
 	var/can_stand
+	var/wound_cleanup_timer
 
 /obj/item/organ/external/Destroy()
 	if(parent && parent.children)
@@ -78,6 +80,10 @@
 		for(var/obj/item/organ/external/C in children)
 			qdel(C)
 
+	if(wound_cleanup_timer)
+		deltimer(wound_cleanup_timer)
+		wound_cleanup_timer = null
+
 	return ..()
 
 /obj/item/organ/external/attackby(obj/item/weapon/W as obj, mob/user as mob)
@@ -392,6 +398,11 @@ This function completely restores a damaged organ to perfect condition.
 		last_dam = brute_dam + burn_dam
 	if(germ_level)
 		return 1
+	if(!wound_cleanup_timer)
+		wound_cleanup_timer = addtimer(src, "cleanup_wounds", SecondsToTicks(600), 1, wounds)
+
+	if (update_icon())
+		owner.UpdateDamageIcon(1)
 	return 0
 
 /obj/item/organ/external/process()
@@ -525,11 +536,6 @@ Note that amputating the affected organ does in fact remove the infection from t
 		return
 
 	for(var/datum/wound/W in wounds)
-		// wounds can disappear after 10 minutes at the earliest
-		if(W.damage <= 0 && W.created + 10 * 10 * 60 <= world.time)
-			wounds -= W
-			continue
-			// let the GC handle the deletion of the wound
 
 		// Internal wounds get worse over time. Low temperatures (cryo) stop them.
 		if(W.internal && !W.can_autoheal() && owner.bodytemperature >= 170)
@@ -941,3 +947,14 @@ Note that amputating the affected organ does in fact remove the infection from t
 	if (!istype(O)) // You're not the primary organ of ANYTHING, bucko
 		return 0
 	return src == O.organs_by_name[limb_name]
+
+// The callback we use to remove wounds from an un-processed limb
+/obj/item/organ/external/proc/cleanup_wounds(var/list/slated_wounds)
+	wound_cleanup_timer = null
+	for(var/datum/wound/W in slated_wounds)
+		if(!W)
+			continue
+		if(W.damage > 0)
+			continue
+		wounds -= W
+		qdel(W)

code/modules/surgery/organs/organ_icon.dm

@@ -1,34 +1,42 @@
 var/global/list/limb_icon_cache = list()
 
 /obj/item/organ/external/proc/compile_icon()
-	overlays.Cut()
+	// I do this so the head's overlays don't get obliterated
+	for(var/child_i in child_icons)
+		overlays -= child_i
+	child_icons.Cut()
 	 // This is a kludge, only one icon has more than one generation of children though.
 	for(var/obj/item/organ/external/organ in contents)
 		if(organ.children && organ.children.len)
 			for(var/obj/item/organ/external/child in organ.children)
 				overlays += child.mob_icon
+				child_icons += child.mob_icon
 		overlays += organ.mob_icon
+		child_icons += organ.mob_icon
 
 /obj/item/organ/external/proc/sync_colour_to_human(var/mob/living/carbon/human/human)
-	s_tone = null
-	s_col = null
 	if(status & ORGAN_ROBOT && !(species && species.name == "Machine")) //machine people get skin color
 		return
 	if(species && human.species && species.name != human.species.name)
 		return
+	if(dna.unique_enzymes != human.dna.unique_enzymes) // This isn't MY arm
+		sync_colour_to_dna()
+		return
 	if(!isnull(human.s_tone) && (human.species.bodyflags & HAS_SKIN_TONE))
+		s_col = null
 		s_tone = human.s_tone
 	if(human.species.bodyflags & HAS_SKIN_COLOR)
+		s_tone = null
 		s_col = list(human.r_skin, human.g_skin, human.b_skin)
 
 /obj/item/organ/external/proc/sync_colour_to_dna()
-	s_tone = null
-	s_col = null
 	if(status & ORGAN_ROBOT)
 		return
 	if(!isnull(dna.GetUIValue(DNA_UI_SKIN_TONE)) && (species.flags & HAS_SKIN_TONE))
+		s_col = null
 		s_tone = dna.GetUIValue(DNA_UI_SKIN_TONE)
 	if(species.flags & HAS_SKIN_COLOR)
+		s_tone = null
 		s_col = list(dna.GetUIValue(DNA_UI_SKIN_R), dna.GetUIValue(DNA_UI_SKIN_G), dna.GetUIValue(DNA_UI_SKIN_B))
 
 /obj/item/organ/external/head/sync_colour_to_human(var/mob/living/carbon/human/human)

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

@@ -194,6 +194,24 @@
 	parent_organ = "head"
 	slot = "eyes"
 
+
+/obj/item/organ/internal/diona_receptor/remove(var/mob/living/user,special = 0)
+	if(!special)
+		owner.disabilities |= NEARSIGHTED
+		owner.sdisabilities |= BLIND
+		owner.eye_blind = 20
+		owner.eye_blurry = 40
+	..()
+
+/obj/item/organ/internal/diona_receptor/surgeryize()
+	if(!owner)
+		return
+	owner.disabilities &= ~NEARSIGHTED
+	owner.sdisabilities &= ~BLIND
+	owner.eye_blurry = 0
+	owner.eye_blind = 0
+
+
 //TODO:Make absorb rads on insert
 
 /obj/item/organ/internal/liver/diona

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

@@ -129,6 +129,26 @@
 	robotize()
 	..()
 
+
+/obj/item/organ/internal/optical_sensor/remove(var/mob/living/user,special = 0)
+	if(!special)
+		owner.disabilities |= NEARSIGHTED
+		owner.sdisabilities |= BLIND
+		owner.eye_blind = 20
+		owner.eye_blurry = 40
+		owner << "Error 404:Optical Sensors not found."
+
+	..()
+
+/obj/item/organ/internal/optical_sensor/surgeryize()
+	if(!owner)
+		return
+	owner.disabilities &= ~NEARSIGHTED
+	owner.sdisabilities &= ~BLIND
+	owner.eye_blurry = 0
+	owner.eye_blind = 0
+
+
 // Used for an MMI or posibrain being installed into a human.
 /obj/item/organ/internal/brain/mmi_holder
 	name = "brain"

code/modules/surgery/other.dm

@@ -2,10 +2,16 @@
 //////////////////////////////////////////////////////////////////
 //					INTERNAL WOUND PATCHING						//
 //////////////////////////////////////////////////////////////////
+
+/datum/surgery/infection
+	name = "external infection treatment/autopsy"
+	steps = list(/datum/surgery_step/generic/cut_open, /datum/surgery_step/generic/cauterize)
+	possible_locs = list("chest","head","groin", "l_arm", "r_arm", "l_leg", "r_leg", "r_hand", "l_hand", "r_foot", "l_foot")
+
 /datum/surgery/bleeding
 	name = "internal bleeding"
 	steps = list(/datum/surgery_step/generic/cut_open,/datum/surgery_step/generic/clamp_bleeders,/datum/surgery_step/generic/retract_skin,/datum/surgery_step/fix_vein,/datum/surgery_step/generic/cauterize)
-	possible_locs = list("chest","head","groin")
+	possible_locs = list("chest","head","groin", "l_arm", "r_arm", "l_leg", "r_leg", "r_hand", "l_hand", "r_foot", "l_foot")
 
 /datum/surgery/bleeding/can_start(mob/user, mob/living/carbon/target)
 	if(ishuman(target))
@@ -14,9 +20,10 @@
 		if(!affected) return 0
 
 		var/internal_bleeding = 0
-		for(var/datum/wound/W in affected.wounds) if(W.internal)
-			internal_bleeding = 1
-			break
+		for(var/datum/wound/W in affected.wounds)
+			if(W.internal)
+				internal_bleeding = 1
+				break
 		if(internal_bleeding)
 			return 1
 		return 0
@@ -37,9 +44,10 @@
 	if(!affected) return 0
 
 	var/internal_bleeding = 0
-	for(var/datum/wound/W in affected.wounds) if(W.internal)
-		internal_bleeding = 1
-		break
+	for(var/datum/wound/W in affected.wounds)
+		if(W.internal)
+			internal_bleeding = 1
+			break
 
 	return affected.open == 2 && internal_bleeding