--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/flux_to_map.py	Sun Oct 13 11:41:34 2024 +0000
@@ -0,0 +1,1055 @@
+from __future__ import division
+import csv
+from enum import Enum
+import re
+import sys
+import numpy as np
+import pandas as pd
+import itertools as it
+import scipy.stats as st
+import lxml.etree as ET
+import math
+import utils.general_utils as utils
+from PIL import Image
+import os
+import copy
+import argparse
+import pyvips
+from PIL import Image, ImageDraw, ImageFont
+from typing import Tuple, Union, Optional, List, Dict
+import matplotlib.pyplot as plt
+
+ERRORS = []
+########################## argparse ##########################################
+ARGS :argparse.Namespace
+def process_args() -> argparse.Namespace:
+    """
+    Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code.
+
+    Args:
+        args : Always obtained (in file) from sys.argv
+
+    Returns:
+        Namespace : An object containing the parsed arguments
+    """
+    parser = argparse.ArgumentParser(
+        usage = "%(prog)s [options]",
+        description = "process some value's genes to create a comparison's map.")
+    
+    #General:
+    parser.add_argument(
+        '-td', '--tool_dir',
+        type = str,
+        required = True,
+        help = 'your tool directory')
+    
+    parser.add_argument('-on', '--control', type = str)
+    parser.add_argument('-ol', '--out_log', help = "Output log")
+
+    #Computation details:
+    parser.add_argument(
+        '-co', '--comparison',
+        type = str, 
+        default = '1vs1',
+        choices = ['manyvsmany', 'onevsrest', 'onevsmany'])
+    
+    parser.add_argument(
+        '-pv' ,'--pValue',
+        type = float, 
+        default = 0.1, 
+        help = 'P-Value threshold (default: %(default)s)')
+    
+    parser.add_argument(
+        '-fc', '--fChange',
+        type = float, 
+        default = 1.5, 
+        help = 'Fold-Change threshold (default: %(default)s)')
+    
+
+    parser.add_argument(
+        '-op', '--option',
+        type = str, 
+        choices = ['datasets', 'dataset_class'],
+        help='dataset or dataset and class')
+
+    parser.add_argument(
+        '-idf', '--input_data_fluxes',
+        type = str,
+        help = 'input dataset fluxes')
+    
+    parser.add_argument(
+        '-icf', '--input_class_fluxes', 
+        type = str,
+        help = 'sample group specification fluxes')
+    
+    parser.add_argument(
+        '-idsf', '--input_datas_fluxes', 
+        type = str,
+        nargs = '+', 
+        help = 'input datasets fluxes')
+    
+    parser.add_argument(
+        '-naf', '--names_fluxes', 
+        type = str,
+        nargs = '+', 
+        help = 'input names fluxes')
+    
+    #Output:
+    parser.add_argument(
+        "-gs", "--generate_svg",
+        type = utils.Bool("generate_svg"), default = True,
+        help = "choose whether to generate svg")
+    
+    parser.add_argument(
+        "-gp", "--generate_pdf",
+        type = utils.Bool("generate_pdf"), default = True,
+        help = "choose whether to generate pdf")
+    
+    parser.add_argument(
+        '-cm', '--custom_map',
+        type = str,
+        help='custom map to use')
+    
+    parser.add_argument(
+        '-mc',  '--choice_map',
+        type = utils.Model, default = utils.Model.HMRcore,
+        choices = [utils.Model.HMRcore, utils.Model.ENGRO2, utils.Model.Custom])
+    
+    parser.add_argument(
+        '-colorm',  '--color_map',
+        type = str,
+        choices = ["jet", "viridis"])
+
+    args :argparse.Namespace = parser.parse_args()
+    args.net = True
+
+    return args
+          
+############################ dataset input ####################################
+def read_dataset(data :str, name :str) -> pd.DataFrame:
+    """
+    Tries to read the dataset from its path (data) as a tsv and turns it into a DataFrame.
+
+    Args:
+        data : filepath of a dataset (from frontend input params or literals upon calling)
+        name : name associated with the dataset (from frontend input params or literals upon calling)
+
+    Returns:
+        pd.DataFrame : dataset in a runtime operable shape
+    
+    Raises:
+        sys.exit : if there's no data (pd.errors.EmptyDataError) or if the dataset has less than 2 columns
+    """
+    try:
+        dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
+    except pd.errors.EmptyDataError:
+        sys.exit('Execution aborted: wrong format of ' + name + '\n')
+    if len(dataset.columns) < 2:
+        sys.exit('Execution aborted: wrong format of ' + name + '\n')
+    return dataset
+
+############################ dataset name #####################################
+def name_dataset(name_data :str, count :int) -> str:
+    """
+    Produces a unique name for a dataset based on what was provided by the user. The default name for any dataset is "Dataset", thus if the user didn't change it this function appends f"_{count}" to make it unique.
+
+    Args:
+        name_data : name associated with the dataset (from frontend input params)
+        count : counter from 1 to make these names unique (external)
+
+    Returns:
+        str : the name made unique
+    """
+    if str(name_data) == 'Dataset':
+        return str(name_data) + '_' + str(count)
+    else:
+        return str(name_data)
+
+############################ map_methods ######################################
+FoldChange = Union[float, int, str] # Union[float, Literal[0, "-INF", "INF"]]
+def fold_change(avg1 :float, avg2 :float) -> FoldChange:
+    """
+    Calculates the fold change between two gene expression values.
+
+    Args:
+        avg1 : average expression value from one dataset avg2 : average expression value from the other dataset
+
+    Returns:
+        FoldChange :
+            0 : when both input values are 0
+            "-INF" : when avg1 is 0
+            "INF" : when avg2 is 0
+            float : for any other combination of values
+    """
+    if avg1 == 0 and avg2 == 0:
+        return 0
+    elif avg1 == 0:
+        return '-INF'
+    elif avg2 == 0:
+        return 'INF'
+    else: # (threshold_F_C - 1) / (abs(threshold_F_C) + 1) con threshold_F_C > 1
+        return (avg1 - avg2) / (abs(avg1) + abs(avg2))
+    
+def fix_style(l :str, col :Optional[str], width :str, dash :str) -> str:
+    """
+    Produces a "fixed" style string to assign to a reaction arrow in the SVG map, assigning style properties to the corresponding values passed as input params.
+
+    Args:
+        l : current style string of an SVG element
+        col : new value for the "stroke" style property
+        width : new value for the "stroke-width" style property
+        dash : new value for the "stroke-dasharray" style property
+
+    Returns:
+        str : the fixed style string
+    """
+    tmp = l.split(';')
+    flag_col = False
+    flag_width = False
+    flag_dash = False
+    for i in range(len(tmp)):
+        if tmp[i].startswith('stroke:'):
+            tmp[i] = 'stroke:' + col
+            flag_col = True
+        if tmp[i].startswith('stroke-width:'):
+            tmp[i] = 'stroke-width:' + width
+            flag_width = True
+        if tmp[i].startswith('stroke-dasharray:'):
+            tmp[i] = 'stroke-dasharray:' + dash
+            flag_dash = True
+    if not flag_col:
+        tmp.append('stroke:' + col)
+    if not flag_width:
+        tmp.append('stroke-width:' + width)
+    if not flag_dash:
+        tmp.append('stroke-dasharray:' + dash)
+    return ';'.join(tmp)
+
+# The type of d values is collapsed, losing precision, because the dict containst lists instead of tuples, please fix!
+def fix_map(d :Dict[str, List[Union[float, FoldChange]]], core_map :ET.ElementTree, threshold_P_V :float, threshold_F_C :float, max_z_score :float) -> ET.ElementTree:
+    """
+    Edits the selected SVG map based on the p-value and fold change data (d) and some significance thresholds also passed as inputs.
+
+    Args:
+        d : dictionary mapping a p-value and a fold-change value (values) to each reaction ID as encoded in the SVG map (keys)
+        core_map : SVG map to modify
+        threshold_P_V : threshold for a p-value to be considered significant
+        threshold_F_C : threshold for a fold change value to be considered significant
+        max_z_score : highest z-score (absolute value)
+    
+    Returns:
+        ET.ElementTree : the modified core_map
+
+    Side effects:
+        core_map : mut
+    """
+    maxT = 12
+    minT = 2
+    grey = '#BEBEBE'
+    blue = '#6495ed'
+    red = '#ecac68'
+    for el in core_map.iter():
+        el_id = str(el.get('id'))
+        if el_id.startswith('R_'):
+            tmp = d.get(el_id[2:])
+            if tmp != None:
+                p_val :float = tmp[0]
+                f_c = tmp[1]
+                z_score = tmp[2]
+                if p_val < threshold_P_V:
+                    if not isinstance(f_c, str):
+                        if abs(f_c) < ((threshold_F_C - 1) / (abs(threshold_F_C) + 1)): # 
+                            col = grey
+                            width = str(minT)
+                        else:
+                            if f_c < 0:
+                                col = blue
+                            elif f_c > 0:
+                                col = red
+                            width = str(max((abs(z_score) * maxT) / max_z_score, minT))
+                    else:
+                        if f_c == '-INF':
+                            col = blue
+                        elif f_c == 'INF':
+                            col = red
+                        width = str(maxT)
+                    dash = 'none'
+                else:
+                    dash = '5,5'
+                    col = grey
+                    width = str(minT)
+                el.set('style', fix_style(el.get('style', ""), col, width, dash))
+    return core_map
+
+def getElementById(reactionId :str, metabMap :ET.ElementTree) -> utils.Result[ET.Element, utils.Result.ResultErr]:
+    """
+    Finds any element in the given map with the given ID. ID uniqueness in an svg file is recommended but
+    not enforced, if more than one element with the exact ID is found only the first will be returned.
+
+    Args:
+        reactionId (str): exact ID of the requested element.
+        metabMap (ET.ElementTree): metabolic map containing the element.
+
+    Returns:
+        utils.Result[ET.Element, ResultErr]: result of the search, either the first match found or a ResultErr.
+    """
+    return utils.Result.Ok(
+        f"//*[@id=\"{reactionId}\"]").map(
+        lambda xPath : metabMap.xpath(xPath)[0]).mapErr(
+        lambda _ : utils.Result.ResultErr(f"No elements with ID \"{reactionId}\" found in map"))
+        # ^^^ we shamelessly ignore the contents of the IndexError, it offers nothing to the user.
+
+def styleMapElement(element :ET.Element, styleStr :str) -> None:
+    currentStyles :str = element.get("style", "")
+    if re.search(r";stroke:[^;]+;stroke-width:[^;]+;stroke-dasharray:[^;]+$", currentStyles):
+        currentStyles = ';'.join(currentStyles.split(';')[:-3])
+
+    element.set("style", currentStyles + styleStr)
+
+class ReactionDirection(Enum):
+    Unknown = ""
+    Direct  = "_F"
+    Inverse = "_B"
+
+    @classmethod
+    def fromDir(cls, s :str) -> "ReactionDirection":
+        # vvv as long as there's so few variants I actually condone the if spam:
+        if s == ReactionDirection.Direct.value:  return ReactionDirection.Direct
+        if s == ReactionDirection.Inverse.value: return ReactionDirection.Inverse
+        return ReactionDirection.Unknown
+
+    @classmethod
+    def fromReactionId(cls, reactionId :str) -> "ReactionDirection":
+        return ReactionDirection.fromDir(reactionId[-2:])
+
+def getArrowBodyElementId(reactionId :str) -> str:
+    if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
+    elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: reactionId = reactionId[:-2]
+    return f"R_{reactionId}"
+
+def getArrowHeadElementId(reactionId :str) -> Tuple[str, str]:
+    """
+    We attempt extracting the direction information from the provided reaction ID, if unsuccessful we provide the IDs of both directions.
+
+    Args:
+        reactionId : the provided reaction ID.
+
+    Returns:
+        Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
+    """
+    if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
+    elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: return reactionId[:-3:-1] + reactionId[:-2], ""
+    return f"F_{reactionId}", f"B_{reactionId}"
+
+class ArrowColor(Enum):
+    """
+    Encodes possible arrow colors based on their meaning in the enrichment process.
+    """
+    Invalid       = "#BEBEBE" # gray, fold-change under treshold
+    Transparent   = "#ffffff00" # white, not significant p-value
+    UpRegulated   = "#ecac68" # red, up-regulated reaction
+    DownRegulated = "#6495ed" # blue, down-regulated reaction
+
+    UpRegulatedInv = "#FF0000"
+    # ^^^ different shade of red (actually orange), up-regulated net value for a reversible reaction with
+    # conflicting enrichment in the two directions.
+
+    DownRegulatedInv = "#0000FF"
+    # ^^^ different shade of blue (actually purple), down-regulated net value for a reversible reaction with
+    # conflicting enrichment in the two directions.
+
+    @classmethod
+    def fromFoldChangeSign(cls, foldChange :float, *, useAltColor = False) -> "ArrowColor":
+        colors = (cls.DownRegulated, cls.DownRegulatedInv) if foldChange < 0 else (cls.UpRegulated, cls.UpRegulatedInv)
+        return colors[useAltColor]
+
+    def __str__(self) -> str: return self.value
+
+class Arrow:
+    """
+    Models the properties of a reaction arrow that change based on enrichment.
+    """
+    MIN_W = 2
+    MAX_W = 12
+
+    def __init__(self, width :int, col: ArrowColor, *, isDashed = False) -> None:
+        """
+        (Private) Initializes an instance of Arrow.
+
+        Args:
+            width : width of the arrow, ideally to be kept within Arrow.MIN_W and Arrow.MAX_W (not enforced).
+            col : color of the arrow.
+            isDashed : whether the arrow should be dashed, meaning the associated pValue resulted not significant.
+        
+        Returns:
+            None : practically, a Arrow instance.
+        """
+        self.w    = width
+        self.col  = col
+        self.dash = isDashed
+    
+    def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
+        if getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).isErr:
+            ERRORS.append(reactionId)
+
+    def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
+        if not mindReactionDir:
+            return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
+        
+        # Now we style the arrow head(s):
+        idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
+        self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
+        if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
+
+    def styleReactionElementsMeanMedian(self, metabMap :ET.ElementTree, reactionId :str, isNegative:bool) -> None:
+
+        self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
+        idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
+
+        if(isNegative):
+            self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
+            self.col = ArrowColor.Transparent
+            self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True)) #trasp
+        else:
+            self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
+            self.col = ArrowColor.Transparent
+            self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True)) #trasp
+
+
+    
+    def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
+        """
+        Computes the reaction ID as encoded in the map for a given reaction ID from the dataset.
+
+        Args:
+            reactionId: the reaction ID, as encoded in the dataset.
+            mindReactionDir: if True forward (F_) and backward (B_) directions will be encoded in the result.
+    
+        Returns:
+            str : the ID of an arrow's body or tips in the map.
+        """
+        # we assume the reactionIds also don't encode reaction dir if they don't mind it when styling the map.
+        if not mindReactionDir: return "R_" + reactionId
+
+        #TODO: this is clearly something we need to make consistent in fluxes
+        return (reactionId[:-3:-1] + reactionId[:-2]) if reactionId[:-2] in ["_F", "_B"] else f"F_{reactionId}" # "Pyr_F" --> "F_Pyr"
+
+    def toStyleStr(self, *, downSizedForTips = False) -> str:
+        """
+        Collapses the styles of this Arrow into a str, ready to be applied as part of the "style" property on an svg element.
+
+        Returns:
+            str : the styles string.
+        """
+        width = self.w
+        if downSizedForTips: width *= 0.8
+        return f";stroke:{self.col};stroke-width:{width};stroke-dasharray:{'5,5' if self.dash else 'none'}"
+
+# vvv These constants could be inside the class itself a static properties, but python
+# was built by brainless organisms so here we are!
+INVALID_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid)
+INSIGNIFICANT_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid, isDashed = True)
+
+def applyFluxesEnrichmentToMap(fluxesEnrichmentRes :Dict[str, Union[Tuple[float, FoldChange], Tuple[float, FoldChange, float, float]]], metabMap :ET.ElementTree, maxNumericZScore :float) -> None:
+    """
+    Applies fluxes enrichment results to the provided metabolic map.
+
+    Args:
+        fluxesEnrichmentRes : fluxes enrichment results.
+        metabMap : the metabolic map to edit.
+        maxNumericZScore : biggest finite z-score value found.
+    
+    Side effects:
+        metabMap : mut
+    
+    Returns:
+        None
+    """
+    for reactionId, values in fluxesEnrichmentRes.items():
+        pValue = values[0]
+        foldChange = values[1]
+        z_score = values[2]
+
+        if isinstance(foldChange, str): foldChange = float(foldChange)
+        if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
+            INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
+            INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
+
+            continue
+
+        if abs(foldChange) <  (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
+            INVALID_ARROW.styleReactionElements(metabMap, reactionId)
+            INVALID_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
+
+            continue
+        
+        width = Arrow.MAX_W
+        if not math.isinf(foldChange):
+            try: 
+                width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W) 
+
+            except ZeroDivisionError: pass
+        
+        #if not reactionId.endswith("_RV"): # RV stands for reversible reactions
+        #    Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId)
+        #    continue
+        
+        #reactionId = reactionId[:-3] # Remove "_RV"
+        
+        inversionScore = (values[3] < 0) + (values[4] < 0) # Compacts the signs of averages into 1 easy to check score
+        if inversionScore == 2: foldChange *= -1
+        # ^^^ Style the inverse direction with the opposite sign netValue
+        
+        # If the score is 1 (opposite signs) we use alternative colors vvv
+        arrow = Arrow(width, ArrowColor.fromFoldChangeSign(foldChange, useAltColor = inversionScore == 1))
+        
+        # vvv These 2 if statements can both be true and can both happen
+        if ARGS.net: # style arrow head(s):
+            arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
+            arrow.applyTo(("F_" if inversionScore == 2 else "B_") + reactionId, metabMap, f";stroke:{ArrowColor.Transparent};stroke-width:0;stroke-dasharray:None")
+
+        arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
+
+
+############################ split class ######################################
+def split_class(classes :pd.DataFrame, resolve_rules :Dict[str, List[float]]) -> Dict[str, List[List[float]]]:
+    """
+    Generates a :dict that groups together data from a :DataFrame based on classes the data is related to.
+
+    Args:
+        classes : a :DataFrame of only string values, containing class information (rows) and keys to query the resolve_rules :dict
+        resolve_rules : a :dict containing :float data
+
+    Returns:
+        dict : the dict with data grouped by class
+
+    Side effects:
+        classes : mut
+    """
+    class_pat :Dict[str, List[List[float]]] = {}
+    for i in range(len(classes)):
+        classe :str = classes.iloc[i, 1]
+        if pd.isnull(classe): continue
+
+        l :List[List[float]] = []
+        for j in range(i, len(classes)):
+            if classes.iloc[j, 1] == classe:
+                pat_id :str = classes.iloc[j, 0]
+                tmp = resolve_rules.get(pat_id, None)
+                if tmp != None:
+                    l.append(tmp)
+                classes.iloc[j, 1] = None
+        
+        if l:
+            class_pat[classe] = list(map(list, zip(*l)))
+            continue
+        
+        utils.logWarning(
+            f"Warning: no sample found in class \"{classe}\", the class has been disregarded", ARGS.out_log)
+    
+    return class_pat
+
+############################ conversion ##############################################
+#conversion from svg to png 
+def svg_to_png_with_background(svg_path :utils.FilePath, png_path :utils.FilePath, dpi :int = 72, scale :int = 1, size :Optional[float] = None) -> None:
+    """
+    Internal utility to convert an SVG to PNG (forced opaque) to aid in PDF conversion.
+
+    Args:
+        svg_path : path to SVG file
+        png_path : path for new PNG file
+        dpi : dots per inch of the generated PNG
+        scale : scaling factor for the generated PNG, computed internally when a size is provided
+        size : final effective width of the generated PNG
+
+    Returns:
+        None
+    """
+    if size:
+        image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=1)
+        scale = size / image.width
+        image = image.resize(scale)
+    else:
+        image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=scale)
+
+    white_background = pyvips.Image.black(image.width, image.height).new_from_image([255, 255, 255])
+    white_background = white_background.affine([scale, 0, 0, scale])
+
+    if white_background.bands != image.bands:
+        white_background = white_background.extract_band(0)
+
+    composite_image = white_background.composite2(image, 'over')
+    composite_image.write_to_file(png_path.show())
+
+#funzione unica, lascio fuori i file e li passo in input
+#conversion from png to pdf
+def convert_png_to_pdf(png_file :utils.FilePath, pdf_file :utils.FilePath) -> None:
+    """
+    Internal utility to convert a PNG to PDF to aid from SVG conversion.
+
+    Args:
+        png_file : path to PNG file
+        pdf_file : path to new PDF file
+
+    Returns:
+        None
+    """
+    image = Image.open(png_file.show())
+    image = image.convert("RGB")
+    image.save(pdf_file.show(), "PDF", resolution=100.0)
+
+#function called to reduce redundancy in the code
+def convert_to_pdf(file_svg :utils.FilePath, file_png :utils.FilePath, file_pdf :utils.FilePath) -> None:
+    """
+    Converts the SVG map at the provided path to PDF.
+
+    Args:
+        file_svg : path to SVG file
+        file_png : path to PNG file
+        file_pdf : path to new PDF file
+
+    Returns:
+        None
+    """
+    svg_to_png_with_background(file_svg, file_png)
+    try:
+        convert_png_to_pdf(file_png, file_pdf)
+        print(f'PDF file {file_pdf.filePath} successfully generated.')
+    
+    except Exception as e:
+        raise utils.DataErr(file_pdf.show(), f'Error generating PDF file: {e}')
+
+############################ map ##############################################
+def buildOutputPath(dataset1Name :str, dataset2Name = "rest", *, details = "", ext :utils.FileFormat) -> utils.FilePath:
+    """
+    Builds a FilePath instance from the names of confronted datasets ready to point to a location in the
+    "result/" folder, used by this tool for output files in collections.
+
+    Args:
+        dataset1Name : _description_
+        dataset2Name : _description_. Defaults to "rest".
+        details : _description_
+        ext : _description_
+
+    Returns:
+        utils.FilePath : _description_
+    """
+    # This function returns a util data structure but is extremely specific to this module.
+    # RAS also uses collections as output and as such might benefit from a method like this, but I'd wait
+    # TODO: until a third tool with multiple outputs appears before porting this to utils.
+    return utils.FilePath(
+        f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
+        # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
+        # all output files: I don't care, this was never the performance bottleneck of the tool and
+        # there is no other net gain in saving and re-using the built string.
+        ext,
+        prefix = "result")
+
+FIELD_NOT_AVAILABLE = '/'
+def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
+    fieldsAmt = len(fieldNames)
+    with open(outPath.show(), "w", newline = "") as fd:
+        writer = csv.DictWriter(fd, fieldnames = fieldNames, delimiter = '\t')
+        writer.writeheader()
+        
+        for row in rows:
+            sizeMismatch = fieldsAmt - len(row)
+            if sizeMismatch > 0: row.extend([FIELD_NOT_AVAILABLE] * sizeMismatch)
+            writer.writerow({ field : data for field, data in zip(fieldNames, row) })
+
+OldEnrichedScores = Dict[str, List[Union[float, FoldChange]]] #TODO: try to use Tuple whenever possible
+def writeTabularResult(enrichedScores : OldEnrichedScores, outPath :utils.FilePath) -> None:
+    fieldNames = ["ids", "P_Value", "fold change"]
+    fieldNames.extend(["average_1", "average_2"])
+
+    writeToCsv([ [reactId] + values for reactId, values in enrichedScores.items() ], fieldNames, outPath)
+
+def temp_thingsInCommon(tmp :Dict[str, List[Union[float, FoldChange]]], core_map :ET.ElementTree, max_z_score :float, dataset1Name :str, dataset2Name = "rest") -> None:
+    # this function compiles the things always in common between comparison modes after enrichment.
+    # TODO: organize, name better.
+    writeTabularResult(tmp, buildOutputPath(dataset1Name, dataset2Name, details = "Tabular Result", ext = utils.FileFormat.TSV))
+    for reactId, enrichData in tmp.items(): tmp[reactId] = tuple(enrichData)
+    applyFluxesEnrichmentToMap(tmp, core_map, max_z_score)
+
+def computePValue(dataset1Data: List[float], dataset2Data: List[float]) -> Tuple[float, float]:
+    """
+    Computes the statistical significance score (P-value) of the comparison between coherent data
+    from two datasets. The data is supposed to, in both datasets:
+    - be related to the same reaction ID;
+    - be ordered by sample, such that the item at position i in both lists is related to the
+      same sample or cell line.
+
+    Args:
+        dataset1Data : data from the 1st dataset.
+        dataset2Data : data from the 2nd dataset.
+
+    Returns:
+        tuple: (P-value, Z-score)
+            - P-value from a Kolmogorov-Smirnov test on the provided data.
+            - Z-score of the difference between means of the two datasets.
+    """
+    # Perform Kolmogorov-Smirnov test
+    ks_statistic, p_value = st.ks_2samp(dataset1Data, dataset2Data)
+    
+    # Calculate means and standard deviations
+    mean1 = np.mean(dataset1Data)
+    mean2 = np.mean(dataset2Data)
+    std1 = np.std(dataset1Data, ddof=1)
+    std2 = np.std(dataset2Data, ddof=1)
+    
+    n1 = len(dataset1Data)
+    n2 = len(dataset2Data)
+    
+    # Calculate Z-score
+    z_score = (mean1 - mean2) / np.sqrt((std1**2 / n1) + (std2**2 / n2))
+    
+    return p_value, z_score
+
+def compareDatasetPair(dataset1Data :List[List[float]], dataset2Data :List[List[float]], ids :List[str]) -> Tuple[Dict[str, List[Union[float, FoldChange]]], float]:
+    #TODO: the following code still suffers from "dumbvarnames-osis"
+    tmp :Dict[str, List[Union[float, FoldChange]]] = {}
+    count   = 0
+    max_z_score = 0
+
+    for l1, l2 in zip(dataset1Data, dataset2Data):
+        reactId = ids[count]
+        count += 1
+        if not reactId: continue # we skip ids that have already been processed
+
+        try: 
+            p_value, z_score = computePValue(l1, l2)
+            avg1 = sum(l1) / len(l1)
+            avg2 = sum(l2) / len(l2)
+            avg = fold_change(avg1, avg2)
+            if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score)
+            tmp[reactId] = [float(p_value), avg, z_score, avg1, avg2]
+        except (TypeError, ZeroDivisionError): continue
+    
+    return tmp, max_z_score
+
+def computeEnrichment(metabMap :ET.ElementTree, class_pat :Dict[str, List[List[float]]], ids :List[str]) -> None:
+    """
+    Compares clustered data based on a given comparison mode and applies enrichment-based styling on the
+    provided metabolic map.
+
+    Args:
+        metabMap : SVG map to modify.
+        class_pat : the clustered data.
+        ids : ids for data association.
+        
+
+    Returns:
+        None
+
+    Raises:
+        sys.exit : if there are less than 2 classes for comparison
+    
+    Side effects:
+        metabMap : mut
+        ids : mut
+    """
+    class_pat = { k.strip() : v for k, v in class_pat.items() }
+    #TODO: simplfy this stuff vvv and stop using sys.exit (raise the correct utils error)
+    if (not class_pat) or (len(class_pat.keys()) < 2): sys.exit('Execution aborted: classes provided for comparisons are less than two\n')
+
+    if ARGS.comparison == "manyvsmany":
+        for i, j in it.combinations(class_pat.keys(), 2):
+            #TODO: these 2 functions are always called in pair and in this order and need common data,
+            # some clever refactoring would be appreciated.
+            comparisonDict, max_z_score = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids)
+            temp_thingsInCommon(comparisonDict, metabMap, max_z_score, i, j)
+    
+    elif ARGS.comparison == "onevsrest":
+        for single_cluster in class_pat.keys():
+            t :List[List[List[float]]] = []
+            for k in class_pat.keys():
+                if k != single_cluster:
+                   t.append(class_pat.get(k))
+            
+            rest :List[List[float]] = []
+            for i in t:
+                rest = rest + i
+            
+            comparisonDict, max_z_score = compareDatasetPair(class_pat.get(single_cluster), rest, ids)
+            temp_thingsInCommon(comparisonDict, metabMap, max_z_score, single_cluster)
+    
+    elif ARGS.comparison == "onevsmany":
+        controlItems = class_pat.get(ARGS.control)
+        for otherDataset in class_pat.keys():
+            if otherDataset == ARGS.control: continue
+            
+            comparisonDict, max_z_score = compareDatasetPair(controlItems, class_pat.get(otherDataset), ids)
+            temp_thingsInCommon(comparisonDict, metabMap, max_z_score, ARGS.control, otherDataset)
+
+def createOutputMaps(dataset1Name :str, dataset2Name :str, core_map :ET.ElementTree) -> None:
+    svgFilePath = buildOutputPath(dataset1Name, dataset2Name, details = "SVG Map", ext = utils.FileFormat.SVG)
+    utils.writeSvg(svgFilePath, core_map)
+
+    if ARGS.generate_pdf:
+        pngPath = buildOutputPath(dataset1Name, dataset2Name, details = "PNG Map", ext = utils.FileFormat.PNG)
+        pdfPath = buildOutputPath(dataset1Name, dataset2Name, details = "PDF Map", ext = utils.FileFormat.PDF)
+        convert_to_pdf(svgFilePath, pngPath, pdfPath)                     
+
+    if not ARGS.generate_svg: os.remove(svgFilePath.show())
+
+ClassPat = Dict[str, List[List[float]]]
+def getClassesAndIdsFromDatasets(datasetsPaths :List[str], datasetPath :str, classPath :str, names :List[str]) -> Tuple[List[str], ClassPat]:
+    # TODO: I suggest creating dicts with ids as keys instead of keeping class_pat and ids separate,
+    # for the sake of everyone's sanity.
+    class_pat :ClassPat = {}
+    if ARGS.option == 'datasets':
+        num = 1 #TODO: the dataset naming function could be a generator
+        for path, name in zip(datasetsPaths, names):
+            name = name_dataset(name, num)
+            resolve_rules_float, ids = getDatasetValues(path, name)
+            if resolve_rules_float != None:
+                class_pat[name] = list(map(list, zip(*resolve_rules_float.values())))
+        
+            num += 1
+    
+    elif ARGS.option == "dataset_class":
+        classes = read_dataset(classPath, "class")
+        classes = classes.astype(str)
+
+        resolve_rules_float, ids = getDatasetValues(datasetPath, "Dataset Class (not actual name)")
+        if resolve_rules_float != None: class_pat = split_class(classes, resolve_rules_float)
+    
+    return ids, class_pat
+    #^^^ TODO: this could be a match statement over an enum, make it happen future marea dev with python 3.12! (it's why I kept the ifs)
+
+#TODO: create these damn args as FilePath objects
+def getDatasetValues(datasetPath :str, datasetName :str) -> Tuple[ClassPat, List[str]]:
+    """
+    Opens the dataset at the given path and extracts the values (expected nullable numerics) and the IDs.
+
+    Args:
+        datasetPath : path to the dataset
+        datasetName (str): dataset name, used in error reporting
+
+    Returns:
+        Tuple[ClassPat, List[str]]: values and IDs extracted from the dataset
+    """
+    dataset = read_dataset(datasetPath, datasetName)
+    IDs = pd.Series.tolist(dataset.iloc[:, 0].astype(str))
+
+    dataset = dataset.drop(dataset.columns[0], axis = "columns").to_dict("list")
+    return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs
+
+def rgb_to_hex(rgb):
+    """
+    Convert RGB values (0-1 range) to hexadecimal color format.
+
+    Args:
+        rgb (numpy.ndarray): An array of RGB color components (in the range [0, 1]).
+
+    Returns:
+        str: The color in hexadecimal format (e.g., '#ff0000' for red).
+    """
+    # Convert RGB values (0-1 range) to hexadecimal format
+    rgb = (np.array(rgb) * 255).astype(int)
+    return '#{:02x}{:02x}{:02x}'.format(rgb[0], rgb[1], rgb[2])
+
+
+
+def save_colormap_image(min_value: float, max_value: float, path: utils.FilePath, colorMap:str="viridis"):
+    """
+    Create and save an image of the colormap showing the gradient and its range.
+
+    Args:
+        min_value (float): The minimum value of the colormap range.
+        max_value (float): The maximum value of the colormap range.
+        filename (str): The filename for saving the image.
+    """
+
+    # Create a colormap using matplotlib
+    cmap = plt.get_cmap(colorMap)
+
+    # Create a figure and axis
+    fig, ax = plt.subplots(figsize=(6, 1))
+    fig.subplots_adjust(bottom=0.5)
+
+    # Create a gradient image
+    gradient = np.linspace(0, 1, 256)
+    gradient = np.vstack((gradient, gradient))
+
+    # Add min and max value annotations
+    ax.text(0, 0.5, f'{np.round(min_value, 3)}', va='center', ha='right', transform=ax.transAxes, fontsize=12, color='black')
+    ax.text(1, 0.5, f'{np.round(max_value, 3)}', va='center', ha='left', transform=ax.transAxes, fontsize=12, color='black')
+
+
+    # Display the gradient image
+    ax.imshow(gradient, aspect='auto', cmap=cmap)
+    ax.set_axis_off()
+
+    # Save the image
+    plt.savefig(path.show(), bbox_inches='tight', pad_inches=0)
+    plt.close()
+    pass
+
+def min_nonzero_abs(arr):
+    # Flatten the array and filter out zeros, then find the minimum of the remaining values
+    non_zero_elements = np.abs(arr)[np.abs(arr) > 0]
+    return np.min(non_zero_elements) if non_zero_elements.size > 0 else None
+
+def computeEnrichmentMeanMedian(metabMap: ET.ElementTree, class_pat: Dict[str, List[List[float]]], ids: List[str], colormap:str) -> None:
+    """
+    Compute and visualize the metabolic map based on mean and median of the input fluxes.
+    The fluxes are normalised across classes/datasets and visualised using the given colormap.
+
+    Args:
+        metabMap (ET.ElementTree): An XML tree representing the metabolic map.
+        class_pat (Dict[str, List[List[float]]]): A dictionary where keys are class names and values are lists of enrichment values.
+        ids (List[str]): A list of reaction IDs to be used for coloring arrows.
+    
+    Returns:
+        None
+    """
+    # Create copies only if they are needed
+    metabMap_mean = copy.deepcopy(metabMap)
+    metabMap_median = copy.deepcopy(metabMap)
+
+    # Compute medians and means
+    medians = {key: np.round(np.median(np.array(value), axis=1), 6) for key, value in class_pat.items()}
+    means = {key: np.round(np.mean(np.array(value), axis=1),6) for key, value in class_pat.items()}
+
+    # Normalize medians and means
+    max_flux_medians = max(np.max(np.abs(arr)) for arr in medians.values())
+    max_flux_means = max(np.max(np.abs(arr)) for arr in means.values())
+
+    min_flux_medians = min(min_nonzero_abs(arr) for arr in medians.values())
+    min_flux_means = min(min_nonzero_abs(arr) for arr in means.values())
+
+    medians = {key: median/max_flux_medians for key, median in medians.items()}
+    means = {key: mean/max_flux_means for key, mean in means.items()}
+
+    save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix="result"), colormap)
+    save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix="result"), colormap)
+
+    cmap = plt.get_cmap(colormap)
+
+    for key in class_pat:
+        # Create color mappings for median and mean
+        colors_median = {
+            rxn_id: rgb_to_hex(cmap(abs(medians[key][i]))) if medians[key][i] != 0 else '#bebebe'  #grey blocked
+            for i, rxn_id in enumerate(ids)
+        }
+
+        colors_mean = {
+            rxn_id: rgb_to_hex(cmap(abs(means[key][i]))) if means[key][i] != 0 else '#bebebe'  #grey blocked
+            for i, rxn_id in enumerate(ids)
+        }
+
+        for i, rxn_id in enumerate(ids):
+            isNegative = medians[key][i] < 0
+
+            # Apply median arrows
+            apply_arrow(metabMap_median, rxn_id, colors_median[rxn_id], isNegative)
+
+            isNegative = means[key][i] < 0
+            # Apply mean arrows
+            apply_arrow(metabMap_mean, rxn_id, colors_mean[rxn_id], isNegative)
+
+        # Save and convert the SVG files
+        save_and_convert(metabMap_mean, "mean", key)
+        save_and_convert(metabMap_median, "median", key)
+
+def apply_arrow(metabMap, rxn_id, color, isNegative):
+    """
+    Apply an arrow to a specific reaction in the metabolic map with a given color.
+
+    Args:
+        metabMap (ET.ElementTree): An XML tree representing the metabolic map.
+        rxn_id (str): The ID of the reaction to which the arrow will be applied.
+        color (str): The color of the arrow in hexadecimal format.
+
+    Returns:
+        None
+    """
+    arrow = Arrow(width=5, col=color)
+    arrow.styleReactionElementsMeanMedian(metabMap, rxn_id, isNegative)
+    pass
+
+def save_and_convert(metabMap, map_type, key):
+    """
+    Save the metabolic map as an SVG file and optionally convert it to PNG and PDF formats.
+
+    Args:
+        metabMap (ET.ElementTree): An XML tree representing the metabolic map.
+        map_type (str): The type of map ('mean' or 'median').
+        key (str): The key identifying the specific map.
+
+    Returns:
+        None
+    """
+    svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix="result")
+    utils.writeSvg(svgFilePath, metabMap)
+    if ARGS.generate_pdf:
+        pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix="result")
+        pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix="result")
+        convert_to_pdf(svgFilePath, pngPath, pdfPath)
+    if not ARGS.generate_svg:
+        os.remove(svgFilePath.show())
+
+
+
+    
+############################ MAIN #############################################
+def main() -> None:
+    """
+    Initializes everything and sets the program in motion based on the fronted input arguments.
+
+    Returns:
+        None
+    
+    Raises:
+        sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
+    """
+
+    global ARGS
+    ARGS = process_args()
+
+    if os.path.isdir('result') == False: os.makedirs('result')
+    
+    core_map :ET.ElementTree = ARGS.choice_map.getMap(
+        ARGS.tool_dir,
+        utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
+    # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.
+    # getMap will None-check the customPath and panic when the model IS custom but there's no file (good). A cleaner
+    # solution can be derived from my comment in FilePath.fromStrPath
+
+    ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas_fluxes, ARGS.input_data_fluxes, ARGS.input_class_fluxes, ARGS.names_fluxes)
+
+    if(ARGS.choice_map == utils.Model.HMRcore):
+        temp_map = utils.Model.HMRcore_no_legend
+        computeEnrichmentMeanMedian(temp_map.getMap(ARGS.tool_dir), class_pat, ids, ARGS.color_map)
+    elif(ARGS.choice_map == utils.Model.ENGRO2):
+        temp_map = utils.Model.ENGRO2_no_legend
+        computeEnrichmentMeanMedian(temp_map.getMap(ARGS.tool_dir), class_pat, ids, ARGS.color_map)
+    else:
+        computeEnrichmentMeanMedian(core_map, class_pat, ids, ARGS.color_map)
+    
+
+    computeEnrichment(core_map, class_pat, ids)
+    
+    # create output files: TODO: this is the same comparison happening in "maps", find a better way to organize this
+    if ARGS.comparison == "manyvsmany":
+        for i, j in it.combinations(class_pat.keys(), 2): createOutputMaps(i, j, core_map)
+        return
+    
+    if ARGS.comparison == "onevsrest":
+        for single_cluster in class_pat.keys(): createOutputMaps(single_cluster, "rest", core_map)
+        return
+    
+    for otherDataset in class_pat.keys():
+        if otherDataset != ARGS.control: createOutputMaps(i, j, core_map)
+
+    if not ERRORS: return
+    utils.logWarning(
+        f"The following reaction IDs were mentioned in the dataset but weren't found in the map: {ERRORS}",
+        ARGS.out_log)
+    
+    print('Execution succeded')
+
+###############################################################################
+if __name__ == "__main__":
+    main()
\ No newline at end of file