Added basic germ code.

This will only trigger in surgery for now - That is when you cut someone open in surgery, you'd better wash your hands before, or otherwise you'll get infected wounds.

code/WorkInProgress/surgery.dm

@@ -57,6 +57,15 @@ proc/build_surgery_steps_list()
 		var/datum/surgery_step/S = new T
 		surgery_steps += S
 
+proc/spread_germs_to_organ(datum/organ/external/E, mob/living/carbon/human/user)
+	if(!istype(user) || !istype(E)) return
+
+	var/germ_level = user.germ_level
+	if(user.gloves)
+		germ_level = user.gloves.germ_level
+
+	E.germ_level = germ_level
+
 
 //////////////////////////////////////////////////////////////////
 //						COMMON STEPS							//
@@ -97,6 +106,7 @@ proc/build_surgery_steps_list()
 		"\blue You have made an incision on [target]'s [affected.display_name] with \the [tool].",)
 		affected.open = 1
 		affected.createwound(CUT, 1)
+		spread_germs_to_organ(affected, user)
 		if (target_zone == "head")
 			target.brain_op_stage = 1
 
@@ -126,6 +136,7 @@ proc/build_surgery_steps_list()
 		"\blue You clamp bleeders in [target]'s [affected.display_name] with \the [tool].")
 		affected.bandage()
 		affected.status &= ~ORGAN_BLEEDING
+		spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -166,6 +177,7 @@ proc/build_surgery_steps_list()
 			self_msg = "\blue You keep the incision open on [target]'s lower abdomen with \the [tool]."
 		user.visible_message(msg, self_msg)
 		affected.open = 2
+		spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -199,6 +211,7 @@ proc/build_surgery_steps_list()
 		user.visible_message("\blue [user] cauterizes the incision on [target]'s [affected.display_name] with \the [tool].", \
 		"\blue You cauterize the incision on [target]'s [affected.display_name] with \the [tool].")
 		affected.open = 0
+		affected.germ_level = 0
 		affected.status &= ~ORGAN_BLEEDING
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
@@ -282,7 +295,7 @@ proc/build_surgery_steps_list()
 
 
 //////////////////////////////////////////////////////////////////
-//				    INTERNAL WOUND PATCHING						//
+//					INTERNAL WOUND PATCHING						//
 //////////////////////////////////////////////////////////////////
 
 
@@ -346,6 +359,7 @@ proc/build_surgery_steps_list()
 		user.visible_message("\blue [user] applies some [tool] to [target]'s bone in [affected.display_name]", \
 			"\blue You apply some [tool] to [target]'s bone in [affected.display_name] with \the [tool].")
 		affected.stage = 1
+		spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -373,10 +387,12 @@ proc/build_surgery_steps_list()
 			user.visible_message("\blue [user] sets the bone in [target]'s [affected.display_name] in place with \the [tool].", \
 				"\blue You set the bone in [target]'s [affected.display_name] in place with \the [tool].")
 			affected.stage = 2
+			spread_germs_to_organ(affected, user)
 		else
 			user.visible_message("\blue [user] sets the bone in [target]'s [affected.display_name]\red in the WRONG place with \the [tool].", \
 				"\blue You set the bone in [target]'s [affected.display_name]\red in the WRONG place with \the [tool].")
 			affected.fracture()
+			spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -403,6 +419,7 @@ proc/build_surgery_steps_list()
 		user.visible_message("\blue [user] sets [target]'s [affected.display_name] skull with \the [tool]." , \
 			"\blue You set [target]'s [affected.display_name] skull with \the [tool].")
 		affected.stage = 2
+		spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -435,6 +452,7 @@ proc/build_surgery_steps_list()
 		affected.status &= ~ORGAN_SPLINTED
 		affected.stage = 0
 		affected.perma_injury = 0
+		spread_germs_to_organ(affected, user)
 
 	fail_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
 		var/datum/organ/external/affected = target.get_organ(target_zone)
@@ -691,7 +709,7 @@ proc/build_surgery_steps_list()
 		"You begin to cut through [target]'s skull with \the [tool].")
 
 	end_step(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool)
-		user.visible_message("\blue [user] has cut through [target]'s skull open with \the [tool].",        \
+		user.visible_message("\blue [user] has cut through [target]'s skull open with \the [tool].",		\
 		"\blue You have cut through [target]'s skull open with \the [tool].")
 		target.brain_op_stage = 2
 
@@ -976,4 +994,4 @@ proc/build_surgery_steps_list()
 		var/datum/organ/external/affected = target.get_organ(target_zone)
 		user.visible_message("\red [user]'s hand slips, damaging connectors on [target]'s [affected.display_name]!", \
 		"\red Your hand slips, damaging connectors on [target]'s [affected.display_name]!")
-		target.apply_damage(10, BRUTE, affected)
+		target.apply_damage(10, BRUTE, affected)

code/datums/organs/organ_external.dm

@@ -33,6 +33,9 @@
 	var/open = 0
 	var/stage = 0
 
+	// INTERNAL germs inside the organ, this is BAD if it's greater 0
+	var/germ_level = 0
+
 		// how often wounds should be updated, a higher number means less often
 	var/wound_update_accuracy = 20 // update every 20 ticks(roughly every minute)
 	New(var/datum/organ/external/P)
@@ -195,6 +198,11 @@
 				// amount of healing is spread over all the wounds
 				W.heal_damage((wound_update_accuracy * amount * W.amount * config.organ_regeneration_multiplier) / (20*owner.number_wounds+1))
 
+			if(W.germ_level > 100 && prob(10))
+				owner.adjustToxLoss(1 * wound_update_accuracy)
+			if(W.germ_level > 1000)
+				owner.adjustToxLoss(1 * wound_update_accuracy)
+
 		// sync the organ's damage with its wounds
 		src.update_damages()
 
@@ -222,6 +230,12 @@
 	proc/get_damage_fire()
 		return burn_dam
 
+	proc/is_infected()
+		for(var/datum/wound/W in wounds)
+			if(W.germ_level > 100)
+				return 1
+		return 0
+
 	process()
 		// process wounds, doing healing etc., only do this every 4 ticks to save processing power
 		if(owner.life_tick % wound_update_accuracy == 0)
@@ -239,6 +253,9 @@
 				return
 		if(config.bones_can_break && brute_dam > min_broken_damage * config.organ_health_multiplier && !(status & ORGAN_ROBOT))
 			src.fracture()
+		if(germ_level > 0)
+			for(var/datum/wound/W in wounds) if(!W.bandaged)
+				W.germ_level = max(W.germ_level, germ_level)
 		return
 
 	proc/fracture()
@@ -694,4 +711,4 @@ obj/item/weapon/organ/r_hand
 	icon_state = "r_hand_l"
 obj/item/weapon/organ/r_leg
 	name = "right leg"
-	icon_state = "r_leg_l"
+	icon_state = "r_leg_l"

code/datums/organs/wound.dm

@@ -41,6 +41,9 @@
 	// internal wounds can only be fixed through surgery
 	var/internal = 0
 
+	// amount of germs in the wound
+	var/germ_level = 0
+
 	// helper lists
 	var/tmp/list/desc_list = list()
 	var/tmp/list/damage_list = list()
@@ -143,7 +146,7 @@
 /datum/wound/gaping_wound
 	max_bleeding_stage = 2
 	stages = list("gaping wound" = 50, "large blood soaked clot" = 25, "large clot" = 15, "small angry scar" = 5, \
-	               "small straight scar" = 0)
+				   "small straight scar" = 0)
 
 /datum/wound/big_gaping_wound
 	max_bleeding_stage = 2
@@ -229,4 +232,4 @@
 	stages = list("severed vein" = 30, "cut vein" = 20, "damaged vein" = 10, "bruised vein" = 5)
 	max_bleeding_stage = 0
 
-	needs_treatment = 1
+	needs_treatment = 1

code/game/atoms.dm

@@ -9,6 +9,7 @@
 	var/last_bumped = 0
 	var/pass_flags = 0
 	var/throwpass = 0
+	var/germ_level = 0 // The higher the germ level, the more germ on the atom.
 
 	///Chemistry.
 	var/datum/reagents/reagents = null
@@ -121,7 +122,7 @@
  * Recursevly searches all atom contens (including contents contents and so on).
  *
  * ARGS: path - search atom contents for atoms of this type
- *       list/filter_path - if set, contents of atoms not of types in this list are excluded from search.
+ *	   list/filter_path - if set, contents of atoms not of types in this list are excluded from search.
  *
  * RETURNS: list of found atoms
  */
@@ -419,8 +420,8 @@ its easier to just keep the beam vertical.
 		A.fingerprints = list()
 	if(!istype(A.fingerprintshidden,/list))
 		A.fingerprintshidden = list()
-	A.fingerprints |= fingerprints            //detective
-	A.fingerprintshidden |= fingerprintshidden    //admin
+	A.fingerprints |= fingerprints			//detective
+	A.fingerprintshidden |= fingerprintshidden	//admin
 	A.fingerprintslast = fingerprintslast
 
 
@@ -555,6 +556,7 @@ its easier to just keep the beam vertical.
 
 /atom/proc/clean_blood()
 	clean_prints()
+	src.germ_level = 0
 	if(istype(blood_DNA, /list))
 		del(blood_DNA)
 		return 1

code/game/objects/items.dm

@@ -221,7 +221,7 @@
 	msg_admin_attack("ATTACK: [user.name] ([user.ckey]) attacked [M.name] ([M.ckey]) with [src.name] (INTENT: [uppertext(user.a_intent)]) (DAMTYE: [uppertext(src.damtype)])") //BS12 EDIT ALG
 
 
-	//spawn(1800)            // this wont work right
+	//spawn(1800)			// this wont work right
 	//	M.lastattacker = null
 	/////////////////////////
 
@@ -624,7 +624,7 @@
 		user << "\red You're going to need to remove that mask/helmet/glasses first."
 		return
 
-	if(istype(M, /mob/living/carbon/alien) || istype(M, /mob/living/carbon/metroid))//Aliens don't have eyes./N     Metroids also don't have eyes!
+	if(istype(M, /mob/living/carbon/alien) || istype(M, /mob/living/carbon/metroid))//Aliens don't have eyes./N	 Metroids also don't have eyes!
 		user << "\red You cannot locate any eyes on this creature!"
 		return
 

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

@@ -138,6 +138,9 @@ MASS SPECTROMETER
 			if(e.status & ORGAN_BROKEN)
 				if(((e.name == "l_arm") || (e.name == "r_arm") || (e.name == "l_leg") || (e.name == "r_leg")) && (!(e.status & ORGAN_SPLINTED)))
 					user << "\red Unsecured fracture in subject [limb]. Splinting recommended for transport."
+			if(e.is_infected())
+				user << "\red Infected wound detected in subject [limb]. Disinfection recommended."
+				
 		for(var/name in H.organs_by_name)
 			var/datum/organ/external/e = H.organs_by_name[name]
 			if(e.status & ORGAN_BROKEN)

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

@@ -353,10 +353,12 @@
 		if(H.gloves)
 			if(H.gloves.clean_blood())
 				H.update_inv_gloves(0)
+			H.gloves.germ_level = 0
 		else
 			if(H.bloody_hands)
 				H.bloody_hands = 0
 				H.update_inv_gloves(0)
+			H.germ_level = 0
 	update_icons()	//apply the now updated overlays to the mob
 
 

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

@@ -280,6 +280,8 @@
 					var/this_wound_desc = W.desc
 					if(W.bleeding()) this_wound_desc = "bleeding [this_wound_desc]"
 					else if(W.bandaged) this_wound_desc = "bandaged [this_wound_desc]"
+					if(W.germ_level > 1000) this_wound_desc = "badly infected [this_wound_desc]"
+					else if(W.germ_level > 100) this_wound_desc = "infected [this_wound_desc]"
 					if(this_wound_desc in wound_descriptors)
 						wound_descriptors[this_wound_desc] += W.amount
 						continue

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

@@ -943,3 +943,10 @@
 	if(wear_suit && wear_suit.flags_inv & HIDEJUMPSUIT && ((head && head.flags_inv & HIDEMASK) || wear_mask))
 		return NEUTER
 	return gender
+
+
+/mob/living/carbon/human/proc/increase_germ_level(n)
+    if(gloves)
+        gloves.germ_level += n
+    else
+        germ_level += n

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

@@ -1166,6 +1166,12 @@
 
 			if(druggy)
 				druggy = max(druggy-1, 0)
+
+			// Increase germ_level by 1 on each life tick
+			germ_level += 1
+			// If you're dirty, your gloves will become dirty, too.
+			if(gloves && germ_level > gloves.germ_level && prob(30))
+				gloves.germ_level += 1
 		return 1
 
 	proc/handle_regular_hud_updates()
@@ -1535,4 +1541,4 @@
 			Paralyse(rand(15,28))
 
 #undef HUMAN_MAX_OXYLOSS
-#undef HUMAN_CRIT_MAX_OXYLOSS
+#undef HUMAN_CRIT_MAX_OXYLOSS