# Pathology Rework Ideas

## Abstract
From what I can remember of the last pathology admin-test, the current pathology code allows singlular bad actors to massacre the station population without offering reasonable opportunities for prevention, mitigation, or RP. In this design doc, I offer some of my broad ideas for revisions to the pathology system to create more engaging gameplay.

I believe the primary job of pathology should be to **investigate unknown cultures shipped from NanoTrasen** and to report back on the symptoms **for a profit**. The secondary job of a pathologist is to **provide proper care for crewmembers who become ill** of space flu, cold, or other common diseases, protecting the crew's overall health. A traitor pathologist should **still be able to cause an epidemic**, but the **crew should be able to protect themselves** (masking) and **survive** with care from the other medical personnel (chem-driven cures).

These opinions may be completely wrong or misdirected, because I do not have much experience with pathology on the servers or on my personal fork. I ask graciously for the reader's patience.

## Goals

Update 1: After searching through the posts related to the earlier Pathology rework attempt, I found several suggestions that are practically identical to what is written here. I will give credit to the forum users by username, and provide links to the suggestion page.

### 1. Connect Medical to Cargo
Suggested previously by [aft2001](https://forum.ss13.co/showthread.php?tid=15693&page=2):

Pathology has the potential to create interdepartmental interaction between medical and cargo. Medbay currently has very little incentive to proactively work with any other department except for damage control. The system I am proposing will give QMs and medical personnel a chance to coordinate.
### 2. Provide a new source of income for the medical department
Suggested previously by [aft2001](https://forum.ss13.co/showthread.php?tid=15693&page=2):

Every productive department (Artsci, botany, chef, rancher, QM, mining, PTL + ordering gas canisters) has some internal mechanism to make money <b> except for medical. </b> Even though genetics has a separate individual price system, the money used by consumers often comes from the stipend payroll and is not "created wealth" like the mentioned examples. I would like to see medical getting its own departmental budget (including genetics) such that crates of pathogens can be ordered from a departmental console. I believe that pathology can be turned into a profitable business venture, shifting the job's focus away from the diseases themselves and toward an economic perspective.
I have relevant comments to make for expanding the departmental budget system to include engineering, service, and science, but that will be in a separate doc.
### 3. ~~Promote the Chain of Command structure within Medical and Command~~ Limit the accessibility of mass-generated pathogens
When a pathogen crate is ordered, ~~various levels of access~~ **a special access permit** should be required to unlock the crate. ~~For three tiers: Tier 1 only requires Pathology access, Tier 2 requires an MD's swipe with a separate Pathology ID, and Tier 3 requires the MD, Pathologist, and another Command ID (maybe add a security ID too)~~. This access requirement allows Pathologists to work on low risk samples without supervision while still allowing for more dangerous viruses through cooperation with supervision from Command personnel. ~~I believe this restriction helps in preventing <b> one person </b> from releasing deathplagues on the crew without declawing the system entirely.~~

Update 1: It's much easier to append the access list with 'permits' for handling each crate tier.

### 4. Make the pathology job analytical instead of manipulating the viruses
I believe the Pathogen Manipulator ~~is~~ poses a serious problem for the system as it allows pathologists to create a highly potent, singular deathstrain. ~~I do not think viruses should be tinkerable: rather,~~ the specimens obtained from cargo should be kept in the genetic condition they were sent. ~~Because high-risk specimens contain fatally dangerous symptoms, a pathologist should not have the equipment to extract the symptoms and alter pathogens.~~ To prevent bad actors from loosing a highly mutatable virus, <b> all viruses should no longer have evolution or mutation.</b> Furthermore, **the number of crate samples pathology can order should be limited** by the market cycle (refreshing every 10-15 minutes) ~~(I suggest 2 or 3)~~. If antagonist pathologists release a low-risk, inherently nonfatal virus, the virus must not be allowed to become fatal through evolution or amplified mutation.

Update 1: I have learned from others' experiences that the key interesting mechanic of pathology was pathogen creation. **I will redesign this mechanic to be more accessible to new players and to strike a balance between player ambitions and resulting game impact.** More to come.

### 5. Eliminate the 'flowchart predictability' of pathology
Symptom catalog previously suggested by [TheMaskedMan2](https://forum.ss13.co/showthread.php?tid=15693&page=4):

One complaint raised in the recent town hall was the boring predictability of the pathology system. One solution to this (assuming pathology will work similar to genetics) is to ~~**completely randomize the solving system for symptoms.**~~ ~~Viruses with different genetic sequencing can still cause the same or very similar symptoms in humans. Analysis should be unique on a sample-to-sample basis.~~

Update 1: While some degree of randomness is necessary, players often want to curate a virus for fun, murder, or otherwise. **To ensure that pathologists do not need to 'roll dice' in order to build the disease they want, a currency/research system similar to genetics will be implemented.** Pathologists would be able to **buy knowledge** about some symptoms, and **unlocking certain higher-tier symptoms** will require reasonable conditions (i.e. publish a perfect report on a pathogen with specific microbody type, report on an inferior symptom to access the superior form, provide blood samples containing X symptoms mixed with X chemical, etc). The design of the new system will allow pathologists to unlock components for pathogen creation in the natural work cycle, and should **let pathologists choose what unlocks to focus on.**

Also, an emagged Pathology console might become the only key to the most devastating symptoms.

### 6. Cut back on the epidemic spread effects
From what I remember of the pathology test round, the viruses spread too fast for anyone to react or engage with before dying or getting stunlocked. Diseases should still be able to spread, but the transmission rate must be simplified and severely reduced. In some circumstances, it may be easier just to not allow spread to occur (i.e. one-off flu/cold, bad hygiene infections) so that pathology and medbay in general is not overwhelmed and the flow of gameplay is not completely stalled.

## Non-Goals

### 1. Completely neuter antagonist Pathologists/MDs
It is extremely important that viruses with bad symptoms can still get released by antagonist Pathologists. Certain symptoms (gibbing) *might* just survive a rework if proper mitigation and vetting mechanisms are introduced. By creating a security system for the antagonist to overcome or get around, antag pathology can still be rewarding (and deadly) without killing **everyone** with viruses.

### 2. Create redundant hoops to jump through
I have suggested multiple IC ways to vet and slow down a pathologist's access to virus samples. I forsee how players may be unwilling to cooperate to access riskier samples, leading to gridlock and dissatisfaction between an MD and pathologists. I think that this conflict can be used as great impetus for RP, but I'm not absolutely sure about this idea. I am certain there are better ways to limit access to dangerous viruses.

### 3. Overrely on pathology to solve problems
Ultimately, pathology should be a subsection of medical, with the main focus on the medbay itself. Although crewmembers should still be able to catch diseases, treatment procedures should not require too much work from the pathologist. Perhaps some coordination between chemistry/pharmacy, medbay, and pathology can be arranged?

## Implementation Example

I have no bearing on the code for pathology. In this section, I will provide a step-by-step description for how a pathologist might go about their job.

### Getting the Sample
Pat the Pathologist, with verbal permission from the MD, orders a high-risk sample crate. The QM sends the crate to medbay. The MD and the captain (or a different command staff) go to pathology to unlock the sample crate with their IDs. Once pathology is clear and Pat is suited up, Pat opens the crate and takes the sample.

### Analyzing the Sample
Pat uses different techniques to analyze the sample. Chemical activators like synthflesh are shot into a petri dish and observed under a microscope, a sample is injected into a monkey and is monitored for visual symptoms, and a genetic sequencing machine to identify all of the symptoms associated with the sample, as well as the potential chemical cure.

### Creating a Report
Pat enters each symptom and the chemical cure into a report-making program on a computer. The computer prints out a large report sticker to be placed on the sample crate. An electronic copy of the report is kept on the computer for reference.

### Profit!
Once the sample is safely locked back in the crate and the monkey is properly disposed of, Pat takes the crate back to the QM office for export. Pat correctly identified all items in the report, so NT delivers the full bounty of 100000 credits for the high-risk analysis. Because Pat swiped to lock and unlock the crate, Pat receives a healthy commission of the 100k reward, with the remainder going to both the medical department budget and the cargo budget.

## Reference Models
Pathology is partially inspired by Plague Inc., as it mirrors the microbody types of the game. It would be wise to continue taking inspiration from this game (specifically with how Plague Inc. handles symptoms).

Roguelike games (FTL, Slay the Spire) implement mutual exclusivity with currency and pathing to give the player choices within a large collection while limiting powercreep and setting the pace of gameplay.

CDDA and Rimworld both feature point systems for character creation, allowing the player to make thoughtful tradeoff decisions for customization. It is not uncommon for new CDDA/Rimworld players to spend a significant amount of their time building characters. This charm was present in pathology and must exist in some form in the rework.

## Changes

### Bugs
~~Here is where I will try to discuss potential problems that will arise:~~
* There is no MD present to unlock medium and high risk samples.
* The MD is the only command staff present.
* A HoP creates the IDs necessary to open high-risk crates.
* The pathologist attempts to brute-force sample information in the report editor.
* The sample is completely used up.
* A sample crate is taken off the Z-level or otherwise destroyed.
* The sample vial is destroyed.
* The report creator is destroyed.
* The sample sticker is destroyed/lost.
* A mechanic scans a virus sample.
* A virus sample is spilled onto a pool of water/blood spanning the entire station.
* A symptom is causing issues to the server performance.
* The incorrect sample was placed in a complete sample crate.
* The Chef deep-fries the vial.
* Something consumes the vial.

Update 1: Let's move these to cover each relevant PR section.

## Potential PRs
**"Pathology should focus on investigating the characteristics of diseases, documenting information for profit and future studies, and providing specialized support when crewmembers catch spaceborne illnesses."**

This statement guides my creative thought process in writing the following suggestion PRs.
### Supply and the CDC: Lootbox Edition

The CDC may outsource pathogen analysis to willing research facilities. Crates delivered should contain a random pathogen sample and have reasonable access restrictions.

Suggested by **@Josephin23**: Medbay should have a dedicated cargo teleport pad for securely transferring CDC crates.

../obj/machinery/computer/QM_supply.dm (lines 21-133)
#### Old GUI
<br>
#### New GUI

### "Simplify" the DNA system

Completely remove pathogen mutation and splicing. Instead of plugging in A-T C-G like genetics, the player assembles a DNA sequence by selecting pathogen characteristics from a known navigable catalog and inputting major characteristics (microbody type, cure, etc). The player is capable of incorrectly labelling symptoms or other values, which results in penalties on the bounty. **Identifying pathogen characteristics builds the final DNA sequence. The sequence itself is for cosmetic purposes only.**

../modules/medical/pathology..
../pathogen.dm (ctrl+f 'mutation')
../pathogen_dna.dm (rebuild ground-up)

Update 1: For the most part, it seems that most of the code for symptoms, transmission, and generation will be intact or foundational. Continuity for gameplay from the last testing session will be a major goal.

### The Pathology Research Console
Turn the Pathology Research+Pathogen Manipulator machines into a glorified report printer. Once a report is finished, a label and a seal can be placed on the inserted vial. The CSS/HTML of pathology overall needs to be modernized using TGUI.

**Remove the splicing/manipulation pages from the console.**

..browserassets/html/pathoComp.html
..browserassets/html/css/pathoui.css

Update 1: The console will also be used to create pathogens with a highly similar gui. More to come.

#### Mockup New UI
<br>
Update 1: Working on a complete overhaul in tgui. I will post it when I learn enough tgui and make a new mockup.

### Rethink pathogen_ailments.dm
There already exists a diseases folder that is used for a large variety of other mechanics (cluwning, heart failure, shock, kuru/poison, vamplague). **Spaceborne illnesses and their symptoms should be immediately differentiable from these implemented disease effects.**

../pathology/pathogen_ailments.dm (entire file)

### Modularize/Tabulate symptoms to be accessible for random pathogen generation and cataloging
The tiering system for CDC pathogen generation is based on the overall danger and number of symptoms in the pathogen. Rebalancing the 'rarity' of symptoms to be more conservative may be necessary, and combining the two symptom files would be cleaner.

../pathology/pathogen_symptoms.dm
../pathology/pathogen_benevolent.dm
### ~~Remove~~ Redesign the Synth-o-matic 6.5.535 pathogen creator
To avoid overcomplexity, cures should be strictly chemical-based similar to the /tg/ virology codebase.

~~**Pathologists can only obtain viruses through the CDC or from natural stationborne outbreaks.**~~
../pathogen_machines.dm (l. 1194-1645)

Update 1: Initially, pathologists should only have to worry about natural or imported strains. Because pathogen creation will remain, refinement in how pathogens interact will be necessary to avoid overstacking diseases and allow for mass voluntary infections (i.e. goodvirus).

### Remove natural pathogen mutation
Pathogen mutation creates snowballing epidemics that harms the flow of gameplay for those who are unprepared. Let mutation remain exclusive to genetics.

../modules/medical/pathology/pathogen.dm (ctrl+f 'mutation')

### Rework transmission
Define a maximum number of 'transmissions' that a disease can spread dependent on active player count. Placing a hardcap on transmission limits the impact of epidemic scenarios and prevents too much disruption in game flow for the whole crew.

../pathology/_pathogen_constants.dm
../pathology/pathogen.dm (ctrl+f 'spread')

Update 1: Futhermore, puddles, clouds, and blood will all be put on hold in favor of functionizing the direct forms of infection, such as aerosol proximity, contact, and ingestion.

# Game Theory and Design

## Machinery

Pathology Research Console: Note: (#) indicates identical horizontal length and vertical alignment. Allows players to insert a reagent beaker when 'chemical cure type' is selected

Top:
- Left: "Pathogen Analyzer"
- Middle: Pathology Research Points
- Right: 'Buy Research Points'

Below Top:
- Left(1): Name of pathogen
- Right(2): Microbody Type (fill-in)

Lower(1), in rows:
- Left: Rank (0,1,2,3,4,5)
- Right: Symptom buttons with text '???' for unknown (bring to rank's symptom catalog)

Lower(2):
- Cure type, w/ subsection box containing:
- if chemical cure, reagent name w/ eject button for beaker
- if thermal cure, either hot or cold
- if surgery, specify which organ replacement
- Transmissions, with list of types in sub-box below
- Finish Report
- View Previous Reports


Pathogen Analyzer: Allows players to insert empty syringes for pathogen analysis.

---

Pathogen Creation Console: A console adjacent to a Path-o-Matic 6.5.535. In TGUI, the interface includes the following sections:

Note: (#) indicates identical horizontal length and vertical alignment.


When a pathogen is created, a report is automatically generated and stored.
**There will be a button to show known and reported diseases for convenient reproduction or for templating.**

Path-o-Matic 2000: Non-interactable machine. Must be adjacent to the Pathogen Creator. Dispenses vials of created pathogen.

---
Microscope: Gives hints on microbody type and symptoms.

Incubator: ???

## Eggs

Ranchers make eggs! Raw eggs can be used as the pathogen growth medium. Let all microbody types use this for petri dish growth, and remove the other specialized growth mediums.

## Pathogen Microbodies

Virus: The most basic type. Cannot **naturally** have T5 symptoms (emag the Pathogen Creator!). Spreads quickly. **Avaliable roundstart** for pathogen creation.

Fungus: Next easiest type. Must be unlocked by researching a fungus-type pathogen. -15% total cost modifier for creation. Advances stages slowly, but **may have T5 symptoms**.

Parasite: Must be unlocked by researching a parasite-type pathogen. Requires double dose of reagent (20u) to cure. May only have chemical cures. Spreads to less people (-2 max infection modifier). +10% to creation cost **and** bounty value. **Can pierce inferior protective clothing.** Cannot naturally have T5 symptoms (emag the Pathogen Creator!).

Bacteria: Last type to unlock, requires fungus and para unlocks + research points. -25% creation cost and bounty value. Cannot naturally have T5 symptoms (emag the Pathogen Creator!).

**Prion**: Traitor Pathologist job specific (5tc). Get 3 sleepypens filled with prion pathogen. Prions attack the brain slowly, eventually killing the infected. Can be suppressed with mannitol, but **cannot be cured**. **Overrides all transmissions, cannot be spread byond Patient 0.**
**If the Pathogen Creator is emagged, a created prion...**

- Can only infect through injection/ingestion (if the symptoms allow it)
- Cannot be detected by health scanners [until postmortem](https://en.wikipedia.org/wiki/Prion#Treatments)
- Can be detected by the Pathogen Analyzer
- +50% increased creation cost
- Uses the standard curing conventions (10u chem or otherwise)
- Follows hierarchy and competition rules (another curing method)
- **May ignore some multipathogen exclusion rules.**

## Emag
Emagging the Pathogen creator or analyzer gives:
- -50% creation cost
- Powerful symptoms unlocked
- Prions and special neurological symptoms

## Symptom Hierarchy, Mutual Exclusivity, and Pathogen Competition
It does not make sense for a single pathogen to have certain combinations of symptoms. For example, a person should not be able to have both mild and serious paranoia, or have superior healing stacked with inferior healing symptoms. When creating a disease, **stronger symptoms should prevent weaker related symptoms from being included**.

Certain symptoms may have effects that, when combined in one pathogen, are overpowered. For example, a pathogen with only Necrotic Preservation and Ressurection would eventually **restore a completely dessicated body to softcrit**. **Pairing this disease with the Regeneration and Anaerobic Resp. mutation would effectively give the player changeling attributes on steroids.** Mutual exclusivity prevents these overpowered situations from occuring automatically (if you can get someone's help to switch from a NecroPres patho to a Res patho, you should still get the same outcome).

The symptom rules for one pathogen should also apply to multiple pathogens in one host. **If a pathogen with 'cough' competes against a pathogen with 'Lung failure', the Lung failure pathogen should outcompete and kill off the cough pathogen.** This is a way to prevent tots or griefers from emagging a market's supply of CDC pathogens and immediately releasing all of them onto the crew to full effect.

Although the strong diseases will survive, those diseases would still have to completely obey mutual exclusivity and hierarchy rules. One hierarchy difference can decide which of two relatively strong pathogens survives. It is still possible to carefully spread out the batch of pathogens to cause bioterror, BUT doing so requires effort from the antagonist to choose a spread of targets and to ensure the targets actually get infected (**splashing only works for fluid-transmissible pathogens**: ingestion or injection is surefire!).

## Pathology Research Points
A currency system where pathologists earn points for accurate CDC reports or by simply paying for points using the research budget directly. This currency system is primarily used for pathogen creation.

Pathology will start with enough points and researched symptoms to create simple viruses. Symptoms are locked sequentially in a Rimworld-esque tech tree with research point costs and prerequisite symptoms. On the Pathogen Creation console, there will be a button leading to a gui containing tabs of the 'tech trees' of symptoms. Hovering over the symptom name gives description info, unlock requirements, and/or cost to unlock.

Some microbody types will be locked via reporting. A pathologist must submit an adequate (50% (?) correct) report on a fungus/parasite/(other locked) pathogen to unlock it for creation. The source of this pathogen may be either stationborne or CDC imported. **In long shifts with natural illnesses, pathology will eventually unlock new microbody types inherently in the process of investigating stationborne pathogens without the need to go through cargo.** The barrier to using different microbody types (and symptoms!) should be generally weak and inline with the fundamental flow of pathology work.

Symptom Documentation
===
Hierarchy follows the magnitude of 'threat': higher threat symptoms exclude lower threat symptoms.

'Buyable' symptoms can be bought roundstart.

## Direct Healing Family

### Brute/Burn Healing

#### Wound Mending
Desc: Slow paced brute damage healing.
Threat: BeneType1
Effect: Heal currentstage/2 amount of brute per lifetick
Reaction: Synthflesh [chem sources of brute]

Buyable.

#### Dermal Restoration
Desc: Slow paced burn damage healing.
Threat: BeneType1
Effect: Heal currentstage/2 amount of burn per lifetick
Reactions: Synthflesh, ClF3 [pyrosium, chem sources of burn]

Buyable.

#### Flesh Restructuring
Desc: Fast paced healing.
Threat: BeneType2
Effect: Heal currentstage/2 amount each of brute, burn per lifetick
Reactions: Synthflesh, sulfuric acid, [other acids]

Research Prereqs: Wound Mending, Dermal Restoration
Cost to unlock after completing prereqs.

---

### Toxin Healing

#### Cleansing
Desc: The pathogen aids in metabolizing ethanol.
Threat: BeneType1
Effect: Deplete ethanol in body by a rate multiplied times currentstage.
Reactions: ethanol [maybe include all alcoholic drinks?]

Buyable.
#### Detoxification
Desc: The pathogen cleans the body of damage caused by toxins.
Threat: BeneType2
Effect: Heal currentstage/2 amount of toxin per tick.
Reactions: Plasma, radium, uranium, [toxin reagents]

Research Prereqs: Cleansing
Cost to unlock after prereqs.

---

### Oxy Healing

#### Sacrificial Respiration
Desc: If the host is in crit and is taking oxydamage, the pathogen will consume the host's flesh (brute+burn) to maintain respiratory flow. (The specific exchange ratio should be such that a person can self-recover from a gradual softcrit.)
Threat: BeneType2
Effect: On crit (hard or soft), increase brute+burn, decrease oxy damage (no bearings on ratio yet).
Reactions, Synthflesh, Oxygen

Prereqs: Wound Mending, Dermal Restor.
Costs to unlock after prereqs.

---

### Ressurection
Desc: The pathogen is symbiotic to the host's central nervous system: if the host dies, the pathogen will attempt to revive the host until the host is too deteriorated (necro).
Threat: BeneType3
Effect: When host is dead, roll to revive into **shallow crit** (heal from deepcrit and differentiate from lings).
Reactions: Synthflesh, StrangeReagent

Prereqs: Flesh Restruc., Sacrificial Resp., Detox.
Costs to unlock.
Mutually exclusive with Necrotic Preservation.

### Necrotic Preservation
Desc: The pathogen will gradually reconstruct a dessicated host corpse to a non-necrotic state.
Threat: BeneType3
Effect: "Reverses necrotic decay" (I need to look into how this is handled).
Reactions: Synthflesh, Formaldehyde

Prereqs: Flesh Restruc., Sacrificial Resp., Detox.
Costs to unlock.
Mutually exclusive with Ressurection.

### Neuron Restoration
Desc: Infection slowly repairs nerve cells in the brain.
Threat: BeneType3
Effect: Roll on lifetick to reduce brain damage.
Reactions: Neurotoxin

Prereqs: Fresh Restruc., Sac. Resp., Detox.
Costs to unlock.

---

## Main Symptom Family

Nausea (1)
Hiccups (2)
Gasping (3)

Runny Nose (1)
Sneezing (2)
Bee Sneeze (3)

"Fluent" (oversalivation) (1)
Cough (2)
Pneumonia (3)
Lung Failure (4)

Ache (1)
Sores (2)
Acute Pain (3)

Itching (1)
Rashes (2)
Jaundice (3)

Indigestion (2)
Stomach Failure (4)

Sweating (2)
Fever (3)
Hyperthermia (4)

Shivering (2)
Chills (3)
Hypothermia (4)

Auto-Brewery (3)
Liver Failure (4)

Appendicitis (3)
Kidney Failure (4)
Leprosy (5)

Teleporting (3)
Genetic Mutation (4)
Radiocative (5)

Capacitor (all subtiers)

---

## Fun Symptom Family
Most of the symptoms here are T0 or T1: competition and hierarchy are reserved for obvious relations. These symptoms are meant to be fun, nonharmful, and nonintrusive to mechanical gameplay.

Shakespearian (this should really be a genetics mutation...)

Sunglasses (0)

Oxytocin Production/Hugging? (0)
Spontaneous flipping (0)
[Emote Stuff]

Balding (0)
Unchecked Hair Growth (0)
[Cosmetic stuff]

---

## Hidden/Emagged Pathogen Creator Symptom Family
These symptoms have an extreme impact on playability. Implementation (if done) of these symptoms should be carefully thought through.

Disorientation (3)
Senility (4)
Episodic Coma (5)

Seizures (5)
Paranoia (5)
Hysteria (5)
Catatonia (5)

Blindness (5)
Deafness (5)

Random Gibbing (?)

---