Configuration

configPath(tokens::Vararg{Union{AbstractString,Integer}})

Return the XML path to the configuration for the given tokens, inferring the path based on the tokens.

This function works by calling the explicit path functions for the given tokens: domainPath, timePath, fullSavePath, svgSavePath, substratePath, cyclePath, apoptosisPath, necrosisPath, volumePath, mechanicsPath, motilityPath, secretionPath, cellInteractionsPath, phagocytosisPath, attackRatePath, fusionPath, transformationPath, integrityPath, customDataPath, initialParameterDistributionPath, and userParameterPath.

This is an experimental feature that can perhaps standardize ways to access the configuration XML path with (hopefully) minimal referencing of the XML file. Take a guess at what you think the inputs should be. Depending on the number of tokens passed in, the function will try to infer the path or throw an error if it cannot. The error message will include the possible tokens that can be used for the given number of tokens as well as the more explicit function that has specific documentation.

rulePath(cell_definition::AbstractString, behavior::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the rule for the given cell type and behavior.

Optionally, add more path_elements to the path as extra arguments.

Example

julia> rulePath("T cell", "attack rate")
2-element Vector{String}:
 "behavior_ruleset:name:T cell"
 "behavior:name:attack rate"

julia> rulePath("cancer", "cycle entry", "increasing_signals", "signal:name:oxygen", "half_max")
5-element Vector{String}:
 "behavior_ruleset:name:cancer"
 "behavior:name:cycle entry"
 "increasing_signals"
 "signal:name:oxygen"
 "half_max"

icCellsPath(cell_definition::AbstractString, patch_type::AbstractString, patch_id, path_elements::Vararg{Union{Integer,AbstractString}})

Return the XML path to the IC cell patch for the given cell type, patch type, and patch ID. The remaining arguments are either just the tag for the patch parameter or the carveout patch type, ID, and tag.

Examples

julia> icCellsPath("default", "disc", 1, "x0")
4-element Vector{String}:
 "cell_patches:name:default"
 "patch_collection:type:disc"
 "patch:ID:1"
 "x0"

julia> icCellsPath("default", "annulus", 1, "rectangle", 1, "width")
7-element Vector{String}:
 "cell_patches:name:default"
 "patch_collection:type:annulus"
 "patch:ID:1"
 "carveout_patches"
 "patch_collection:type:rectangle"
 "patch:ID:1"
 "width"

icECMPath(layer_id::Int, patch_type::AbstractString, patch_id, path_elements::Vararg{AbstractString})

Return the XML path to the IC ECM patch for the given layerid, patchtype, and patchid. Optionally, add more pathelements to the path as extra arguments.

Examples

julia> icECMPath(2, "ellipse", 1, "a")
4-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:ellipse"
 "patch:ID:1"
 "a"

julia> icECMPath(2, "elliptical_disc", 1, "density")
4-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:elliptical_disc"
 "patch:ID:1"
 "density"

julia> icECMPath(2, "ellipse_with_shell", 1, "interior", "density")
5-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:ellipse_with_shell"
 "patch:ID:1"
 "interior"
 "density"

domainPath(tag::AbstractString)

Return the XML path to the domain for the given tag.

Possible tags include:

• "x_min"
• "x_max"
• "y_min"
• "y_max"
• "z_min"
• "z_max"
• "dx"
• "dy"
• "dz"
• "use_2D" (value is "true"or "false")

timePath(tag::AbstractString)

Return the XML path to the time for the given tag.

Possible tags include:

• "max_time"
• "dt_intracellular"
• "dt_diffusion"
• "dt_mechanics"
• "dt_phenotype"

fullSavePath()

Return the XML path to the interval for full data saves.

svgSavePath()

Return the XML path to the interval for SVG data saves.

substratePath(substrate_name::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the substrate for the given name (or deeper if more path elements are given).

Possible path_elements include:

• substratePath(<substrate_name>, "physical_parameter_set", <tag>) with <tag> one of
  • "diffusion_coefficient"
  • "decay_rate"
• substratePath(<substrate_name>, <tag>) with <tag> one of
  • "initial_condition"
  • "Dirichlet_boundary_condition"
• substratePath(<substrate_name>, "Dirichlet_options", "boundary_value:ID:<boundary_id>") where <boundary_id> is one of
  • "xmin"
  • "xmax"
  • "ymin"
  • "ymax"
  • "zmin"
  • "zmax"

cyclePath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the cycle for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• cyclePath(<cell_type>, "phase_durations", "duration:index:0") # replace 0 with the index of the phase
• cyclePath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # replace 0 with the start index of the phase

apoptosisPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the apoptosis for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• apoptosisPath(<cell_type>, "death_rate")
• apoptosisPath(<cell_type>, "phase_durations", "duration:index:0") # apoptosis only has one phase, so index is always 0
• apoptosisPath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # apoptosis only has one phase, so start index is always 0
• apoptosisPath(<cell_type>, "parameters", <tag>) with <tag> one of
  • unlysed_fluid_change_rate
  • lysed_fluid_change_rate
  • cytoplasmic_biomass_change_rate
  • nuclear_biomass_change_rate
  • calcification_rate
  • relative_rupture_volume

necrosisPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the necrosis for the given cell type (or deeper if more path elements are given).

Possible path_elements are identical to those for apoptosisPath with one exception: Necrosis has two phases so the phase index can be either 0 or 1. They include:

• necrosisPath(<cell_type>, "death_rate")
• necrosisPath(<cell_type>, "phase_durations", "duration:index:0") # necrosis has two phases, so index is either 0 or 1
• necrosisPath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # necrosis has two phases, so start index is either 0 or 1
• necrosisPath(<cell_type>, "parameters", <tag>) with <tag> one of
  • unlysed_fluid_change_rate
  • lysed_fluid_change_rate
  • cytoplasmic_biomass_change_rate
  • nuclear_biomass_change_rate
  • calcification_rate
  • relative_rupture_volume

volumePath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the volume for the given cell type (or deeper if more path elements are given).

Possible tags include:

• "total"
• "fluid_fraction"
• "nuclear"
• "fluid_change_rate"
• "cytoplasmic_biomass_change_rate"
• "nuclear_biomass_change_rate"
• "calcified_fraction"
• "calcification_rate"
• "relative_rupture_volume"

mechanicsPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the mechanics for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• mechanicsPath(<cell_type>, <tag>) with <tag> one of
  • "cell_cell_adhesion_strength"
  • "cell_cell_repulsion_strength"
  • "relative_maximum_adhesion_distance"
  • "attachment_elastic_constant"
  • "attachment_rate"
  • "detachment_rate"
  • "maximum_number_of_attachments"
• mechanicsPath(<cell_type>, "cell_adhesion_affinities", "cell_adhesion_affinity:name:<cell_type>")
  • <cell_type> is a string of the model cell type
• mechanicsPath(<cell_type>, "options", <tag>) with <tag> one of
  • "set_relative_equilibrium_distance"
  • "set_absolute_equilibrium_distance"

motilityPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the motility for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• motilityPath(<cell_type>, <tag>) with <tag> one of
  • "speed"
  • "persistence_time"
  • "migration_bias"
• motilityPath(<cell_type>, "options", <tag>) with <tag> one of
  • "enabled" (value is "true"or "false")
  • "use_2D" (value is "true"or "false")
• motilityPath(<cell_type>, "options", "chemotaxis", <tag>) with <tag> one of
  • "enabled" (value is "true"or "false")
  • "substrate" (value is string of the model substrate)
  • "direction" (value is -1 or 1)
• motilityPath(<cell_type>, "options", "advanced_chemotaxis", <tag>)
  • "enabled" (value is "true"or "false")
  • "normalize_each_gradient" (value is "true"or "false")
• motilityPath(<cell_type>, "options", "advanced_chemotaxis", "chemotactic_sensitivities", "chemotactic_sensitivity:substrate:<substrate_name>")
  • <substrate_name> is a string of the model substrate

secretionPath(cell_definition::AbstractString, substrate_name::AbstractString, tag::AbstractString)

Return the XML path to the secretion tag of the given substrate for the given cell type.

Possible tags include:

• "secretion_rate"
• "secretion_target"
• "uptake_rate"
• "net_export_rate"

cellInteractionsPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the cell interactions for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• cellInteractionsPath(<cell_type>, <tag>) with <tag> one of
  • "apoptotic_phagocytosis_rate"
  • "necrotic_phagocytosis_rate"
  • "other_dead_phagocytosis_rate"
  • "attack_damage_rate"
  • "attack_duration"

For other elements in <cell_interactions>, use phagocytosisPath, attackRatePath, or fusionPath as needed.

phagocytosisPath(cell_definition::AbstractString, target_cell_definition::AbstractString)
phagocytosisPath(cell_definition::AbstractString, death_process::Symbol)

Return the XML path to the phagocytosis element for the given cell type. If a string is supplied, it is treated as a cell type. If a symbol is supplied, it specifies a death model and must be one of :apoptosis, :necrosis, or :other_dead.

Examples

julia> PhysiCellModelManager.phagocytosisPath("M1", "cancer")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:M1"
 "phenotype"
 "cell_interactions"
 "live_phagocytosis_rates"
 "phagocytosis_rate:name:cancer"

julia> PhysiCellModelManager.phagocytosisPath("M1", :apoptotic)
5-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:M1"
 "phenotype"
 "cell_interactions"
 "apoptotic_phagocytosis_rate"

attackRatePath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Return the XML path to the attack rate of the first cell type attacking the second cell type. attackPath and attackRatesPath are synonyms for this function.

Examples

julia> PhysiCellModelManager.attackRatePath("cd8", "cancer")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:cd8"
 "phenotype"
 "cell_interactions"
 "attack_rates"
 "attack_rate:name:cancer"

fusionPath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Return the XML path to the fusion rate of the first cell type fusing to the second cell type.

Examples

julia> PhysiCellModelManager.fusionPath("epi", "epi")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:epi"
 "phenotype"
 "cell_interactions"
 "fusion_rates"
 "fusion_rate:name:epi"

integrityPath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the cell integrity tag for the given cell type.

Possible tags include:

• "damage_rate"
• "damage_repair_rate"

customDataPath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the custom data tag for the given cell type.

initialParameterDistributionPath(cell_definition::AbstractString, behavior::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the initial parameter distribution of the behavior for the given cell type.

Possible path_elements depend on the type of the distribution:

• type="Uniform" : min, max
• type="LogUniform" : min, max
• type="Normal" : mu, sigma, lower_bound, upper_bound
• type="LogNormal" : mu, sigma, lower_bound, upper_bound
• type="Log10Normal": mu, sigma, lower_bound, upper_bound

userParameterPath(tag::AbstractString)

Return the XML path to the user parameter for the given field name. userParametersPath is a synonym for this function.

apoptosisPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the apoptosis for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• apoptosisPath(<cell_type>, "death_rate")
• apoptosisPath(<cell_type>, "phase_durations", "duration:index:0") # apoptosis only has one phase, so index is always 0
• apoptosisPath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # apoptosis only has one phase, so start index is always 0
• apoptosisPath(<cell_type>, "parameters", <tag>) with <tag> one of
  • unlysed_fluid_change_rate
  • lysed_fluid_change_rate
  • cytoplasmic_biomass_change_rate
  • nuclear_biomass_change_rate
  • calcification_rate
  • relative_rupture_volume

attackRatePath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Return the XML path to the attack rate of the first cell type attacking the second cell type. attackPath and attackRatesPath are synonyms for this function.

Examples

julia> PhysiCellModelManager.attackRatePath("cd8", "cancer")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:cd8"
 "phenotype"
 "cell_interactions"
 "attack_rates"
 "attack_rate:name:cancer"

cellDefinitionPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the cell definition or deeper if more path elements are given.

cellInteractionsPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the cell interactions for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• cellInteractionsPath(<cell_type>, <tag>) with <tag> one of
  • "apoptotic_phagocytosis_rate"
  • "necrotic_phagocytosis_rate"
  • "other_dead_phagocytosis_rate"
  • "attack_damage_rate"
  • "attack_duration"

For other elements in <cell_interactions>, use phagocytosisPath, attackRatePath, or fusionPath as needed.

configPath(tokens::Vararg{Union{AbstractString,Integer}})

Return the XML path to the configuration for the given tokens, inferring the path based on the tokens.

This function works by calling the explicit path functions for the given tokens: domainPath, timePath, fullSavePath, svgSavePath, substratePath, cyclePath, apoptosisPath, necrosisPath, volumePath, mechanicsPath, motilityPath, secretionPath, cellInteractionsPath, phagocytosisPath, attackRatePath, fusionPath, transformationPath, integrityPath, customDataPath, initialParameterDistributionPath, and userParameterPath.

This is an experimental feature that can perhaps standardize ways to access the configuration XML path with (hopefully) minimal referencing of the XML file. Take a guess at what you think the inputs should be. Depending on the number of tokens passed in, the function will try to infer the path or throw an error if it cannot. The error message will include the possible tokens that can be used for the given number of tokens as well as the more explicit function that has specific documentation.

customDataPath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the custom data tag for the given cell type.

cyclePath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the cycle for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• cyclePath(<cell_type>, "phase_durations", "duration:index:0") # replace 0 with the index of the phase
• cyclePath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # replace 0 with the start index of the phase

domainPath(tag::AbstractString)

Return the XML path to the domain for the given tag.

Possible tags include:

• "x_min"
• "x_max"
• "y_min"
• "y_max"
• "z_min"
• "z_max"
• "dx"
• "dy"
• "dz"
• "use_2D" (value is "true"or "false")

fullSavePath()

Return the XML path to the interval for full data saves.

fusionPath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Return the XML path to the fusion rate of the first cell type fusing to the second cell type.

Examples

julia> PhysiCellModelManager.fusionPath("epi", "epi")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:epi"
 "phenotype"
 "cell_interactions"
 "fusion_rates"
 "fusion_rate:name:epi"

icCellsPath(cell_definition::AbstractString, patch_type::AbstractString, patch_id, path_elements::Vararg{Union{Integer,AbstractString}})

Return the XML path to the IC cell patch for the given cell type, patch type, and patch ID. The remaining arguments are either just the tag for the patch parameter or the carveout patch type, ID, and tag.

Examples

julia> icCellsPath("default", "disc", 1, "x0")
4-element Vector{String}:
 "cell_patches:name:default"
 "patch_collection:type:disc"
 "patch:ID:1"
 "x0"

julia> icCellsPath("default", "annulus", 1, "rectangle", 1, "width")
7-element Vector{String}:
 "cell_patches:name:default"
 "patch_collection:type:annulus"
 "patch:ID:1"
 "carveout_patches"
 "patch_collection:type:rectangle"
 "patch:ID:1"
 "width"

icECMPath(layer_id::Int, patch_type::AbstractString, patch_id, path_elements::Vararg{AbstractString})

Return the XML path to the IC ECM patch for the given layerid, patchtype, and patchid. Optionally, add more pathelements to the path as extra arguments.

Examples

julia> icECMPath(2, "ellipse", 1, "a")
4-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:ellipse"
 "patch:ID:1"
 "a"

julia> icECMPath(2, "elliptical_disc", 1, "density")
4-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:elliptical_disc"
 "patch:ID:1"
 "density"

julia> icECMPath(2, "ellipse_with_shell", 1, "interior", "density")
5-element Vector{String}:
 "layer:ID:2"
 "patch_collection:type:ellipse_with_shell"
 "patch:ID:1"
 "interior"
 "density"

initialParameterDistributionPath(cell_definition::AbstractString, behavior::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the initial parameter distribution of the behavior for the given cell type.

Possible path_elements depend on the type of the distribution:

• type="Uniform" : min, max
• type="LogUniform" : min, max
• type="Normal" : mu, sigma, lower_bound, upper_bound
• type="LogNormal" : mu, sigma, lower_bound, upper_bound
• type="Log10Normal": mu, sigma, lower_bound, upper_bound

integrityPath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the cell integrity tag for the given cell type.

Possible tags include:

• "damage_rate"
• "damage_repair_rate"

mechanicsPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the mechanics for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• mechanicsPath(<cell_type>, <tag>) with <tag> one of
  • "cell_cell_adhesion_strength"
  • "cell_cell_repulsion_strength"
  • "relative_maximum_adhesion_distance"
  • "attachment_elastic_constant"
  • "attachment_rate"
  • "detachment_rate"
  • "maximum_number_of_attachments"
• mechanicsPath(<cell_type>, "cell_adhesion_affinities", "cell_adhesion_affinity:name:<cell_type>")
  • <cell_type> is a string of the model cell type
• mechanicsPath(<cell_type>, "options", <tag>) with <tag> one of
  • "set_relative_equilibrium_distance"
  • "set_absolute_equilibrium_distance"

motilityPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the motility for the given cell type (or deeper if more path elements are given).

Possible path_elements include:

• motilityPath(<cell_type>, <tag>) with <tag> one of
  • "speed"
  • "persistence_time"
  • "migration_bias"
• motilityPath(<cell_type>, "options", <tag>) with <tag> one of
  • "enabled" (value is "true"or "false")
  • "use_2D" (value is "true"or "false")
• motilityPath(<cell_type>, "options", "chemotaxis", <tag>) with <tag> one of
  • "enabled" (value is "true"or "false")
  • "substrate" (value is string of the model substrate)
  • "direction" (value is -1 or 1)
• motilityPath(<cell_type>, "options", "advanced_chemotaxis", <tag>)
  • "enabled" (value is "true"or "false")
  • "normalize_each_gradient" (value is "true"or "false")
• motilityPath(<cell_type>, "options", "advanced_chemotaxis", "chemotactic_sensitivities", "chemotactic_sensitivity:substrate:<substrate_name>")
  • <substrate_name> is a string of the model substrate

necrosisPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the necrosis for the given cell type (or deeper if more path elements are given).

Possible path_elements are identical to those for apoptosisPath with one exception: Necrosis has two phases so the phase index can be either 0 or 1. They include:

• necrosisPath(<cell_type>, "death_rate")
• necrosisPath(<cell_type>, "phase_durations", "duration:index:0") # necrosis has two phases, so index is either 0 or 1
• necrosisPath(<cell_type>, "phase_transition_rates", "rate:start_index:0") # necrosis has two phases, so start index is either 0 or 1
• necrosisPath(<cell_type>, "parameters", <tag>) with <tag> one of
  • unlysed_fluid_change_rate
  • lysed_fluid_change_rate
  • cytoplasmic_biomass_change_rate
  • nuclear_biomass_change_rate
  • calcification_rate
  • relative_rupture_volume

phagocytosisPath(cell_definition::AbstractString, target_cell_definition::AbstractString)
phagocytosisPath(cell_definition::AbstractString, death_process::Symbol)

Return the XML path to the phagocytosis element for the given cell type. If a string is supplied, it is treated as a cell type. If a symbol is supplied, it specifies a death model and must be one of :apoptosis, :necrosis, or :other_dead.

Examples

julia> PhysiCellModelManager.phagocytosisPath("M1", "cancer")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:M1"
 "phenotype"
 "cell_interactions"
 "live_phagocytosis_rates"
 "phagocytosis_rate:name:cancer"

julia> PhysiCellModelManager.phagocytosisPath("M1", :apoptotic)
5-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:M1"
 "phenotype"
 "cell_interactions"
 "apoptotic_phagocytosis_rate"

phenotypePath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the phenotype for the given cell type (or deeper if more path elements are given).

rulePath(cell_definition::AbstractString, behavior::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the rule for the given cell type and behavior.

Optionally, add more path_elements to the path as extra arguments.

Example

julia> rulePath("T cell", "attack rate")
2-element Vector{String}:
 "behavior_ruleset:name:T cell"
 "behavior:name:attack rate"

julia> rulePath("cancer", "cycle entry", "increasing_signals", "signal:name:oxygen", "half_max")
5-element Vector{String}:
 "behavior_ruleset:name:cancer"
 "behavior:name:cycle entry"
 "increasing_signals"
 "signal:name:oxygen"
 "half_max"

secretionPath(cell_definition::AbstractString, substrate_name::AbstractString, tag::AbstractString)

Return the XML path to the secretion tag of the given substrate for the given cell type.

Possible tags include:

• "secretion_rate"
• "secretion_target"
• "uptake_rate"
• "net_export_rate"

substratePath(substrate_name::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the substrate for the given name (or deeper if more path elements are given).

Possible path_elements include:

• substratePath(<substrate_name>, "physical_parameter_set", <tag>) with <tag> one of
  • "diffusion_coefficient"
  • "decay_rate"
• substratePath(<substrate_name>, <tag>) with <tag> one of
  • "initial_condition"
  • "Dirichlet_boundary_condition"
• substratePath(<substrate_name>, "Dirichlet_options", "boundary_value:ID:<boundary_id>") where <boundary_id> is one of
  • "xmin"
  • "xmax"
  • "ymin"
  • "ymax"
  • "zmin"
  • "zmax"

svgSavePath()

Return the XML path to the interval for SVG data saves.

timePath(tag::AbstractString)

Return the XML path to the time for the given tag.

Possible tags include:

• "max_time"
• "dt_intracellular"
• "dt_diffusion"
• "dt_mechanics"
• "dt_phenotype"

transformationPath(from_cell_definition::AbstractString, to_cell_definition::AbstractString)

Return the XML path to the transformation rates for the first cell definition to the second cell definition.

Examples

julia> PhysiCellModelManager.transformationPath("M1", "M2")
6-element Vector{String}:
 "cell_definitions"
 "cell_definition:name:M1"
 "phenotype"
 "cell_transformations"
 "transformation_rates"
 "transformation_rate:name:M2"

userParameterPath(tag::AbstractString)

Return the XML path to the user parameter for the given field name. userParametersPath is a synonym for this function.

volumePath(cell_definition::AbstractString, tag::AbstractString)

Return the XML path to the volume for the given cell type (or deeper if more path elements are given).

Possible tags include:

• "total"
• "fluid_fraction"
• "nuclear"
• "fluid_change_rate"
• "cytoplasmic_biomass_change_rate"
• "nuclear_biomass_change_rate"
• "calcified_fraction"
• "calcification_rate"
• "relative_rupture_volume"

ProjectLocations

A struct that contains information about the locations of input files in the project.

The global instance of this struct is project_locations in pcmm_globals (the sole instance of PCMMGlobals) and is created by reading the inputs.toml file in the data directory. It is instantiated with the parseProjectInputsConfigurationFile function.

Fields

• all::NTuple{L,Symbol}: A tuple of all locations in the project.
• required::NTuple{M,Symbol}: A tuple of required locations in the project.
• varied::NTuple{N,Symbol}: A tuple of varied locations in the project.

attackPath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Alias for attackRatePath.

attackRatesPath(cell_definition::AbstractString, target_cell_definition::AbstractString)

Alias for attackRatePath.

cellParameterName(column_name::String)

Return the short name of the varied parameter associated with a cell definition for the given column name used in creating a DataFrame summary table.

columnName(xml_path)

Return the column name corresponding to the given XML path.

Works on a vector of strings, an XMLPath object, or a ElementaryVariation object. Inverse of columnNameToXMLPath.

columnNameToXMLPath(column_name::String)

Return the XML path corresponding to the given column name.

Inverse of columnName.

createInputsTOMLTemplate(path_to_toml::String)

Create a template TOML file for the inputs configuration at the specified path.

This is something users should not be changing. It is something in the codebase to hopefully facilitate extending this framework to other ABM frameworks.

createXMLFile(location::Symbol, M::AbstractMonad)

Create XML file for the given location and variation_id in the given monad.

The file is placed in $(location)_variations and can be accessed from there to run the simulation(s).

deathPath(cell_definition::AbstractString, path_elements::Vararg{AbstractString})

Return the XML path to the death for the given cell type (or deeper if more path elements are given). Users are encouraged to use the apoptosisPath or necrosisPath functions.

elementIsTerminal(e::XMLElement)

Check if an XML element is terminal (i.e., has no child elements). Returns true if the element has no children, false otherwise.

folderIsVaried(location::Symbol, folder::String)

Return true if the location folder allows for varying the input files, false otherwise.

getChildByAttribute(parent_element::XMLElement, path_element_split::Vector{<:AbstractString})

Get the child element of parent_element that matches the given tag and attribute.

getChildByChildContent(current_element::XMLElement, path_element::AbstractString)

Get the child element of current_element that matches the given tag and child content.

getSimpleContent(xml_doc::XMLDocument, xml_path::Vector{<:AbstractString}; required::Bool=true)

Get the content of the element in the XML document that matches the given path. See retrieveElement.

Validates that the element is terminal (has no child elements) and contains non-empty text content. Throws AssertionError if either condition is not met.

icCellParameterName(name::String)

Return the short name of the varied parameter associated with a cell patch for the given name used in creating a DataFrame summary table.

icECMParameterName(name::String)

Return the short name of the varied parameter associated with a ECM patch for the given name used in creating a DataFrame summary table.

inferDeathModelPath(death_model::Symbol, token1::AbstractString, token3::AbstractString)

Helper function to infer the death model path based on the death model and the third token passed in to configPath.

locationFolder(location::Union{String,Symbol})

Return the name of the folder for the location (as either a String or Symbol). This is the folder where the directories with the input files for the location are stored.

locationIDName(location)

Return the name of the ID column for the location (as either a String or Symbol).

Examples

julia> PhysiCellModelManager.locationIDName(:config)
"config_id"

locationIDNames()

Return the names of the ID columns for all locations.

locationPath(location::Symbol, folder=missing)

Return the path to the location folder in the inputs directory.

If folder is not specified, the path to the location folder is returned.

locationPath(input_folder::InputFolder)

Return the path to the location folder in the inputs directory for the InputFolder object.

locationPath(location::Symbol, S::AbstractSampling)

Return the path to the location folder in the inputs directory for the AbstractSampling object.

locationTableName(location)

Return the name of the table for the location (as either a String or Symbol). This table stores the folder names and their IDs for the location.

Examples

julia> PhysiCellModelManager.locationTableName(:config)
"configs"

locationVariationIDName(location)

Return the name of the variation ID column for the location (as either a String or Symbol).

Examples

julia> PhysiCellModelManager.locationVariationIDName(:config)
"config_variation_id"

locationVariationIDNames()

Return the names of the variation ID columns for all varied locations.

locationVariationsDBName(location::Union{String,Symbol})

Return the name of the variations database for the location (as either a String or Symbol).

locationVariationsFolder(location)

Return the name of the variations folder for the location (as either a String or Symbol).

locationVariationsTableName(location)

Return the name of the variations table for the location (as either a String or Symbol). This table stores the variations of the folder it is located in.

makeXMLPath(xml_doc::XMLDocument, xml_path::AbstractVector{<:AbstractString})

Create (if it does not exist) and return the XML element relative to the root of the given XML document.

Arguments

• xml_doc::XMLDocument: The XML document to start from.
• xml_path::AbstractVector{<:AbstractString}: The path to the XML element to create or retrieve. Can be a string representing a child of the root element.

makeXMLPath(current_element::XMLElement, xml_path::AbstractVector{<:AbstractString})

Create (if it does not exist) and return the XML element relative to the given XML element.

Similar functionality to the shell command mkdir -p, but for XML elements.

Arguments

• current_element::XMLElement: The current XML element to start from.
• xml_path::AbstractVector{<:AbstractString}: The path to the XML element to create or retrieve. Can be a string representing a child of the current element.

parseProjectInputsConfigurationFile()

Parse the inputs.toml file in the data directory and create a global ProjectLocations object.

pathToInputsConfig()

Return the path to the inputs.toml file in the inputs directory.

postVariationXMLProcessing(location::Symbol, path_to_xml::String)

Perform any post-processing needed after creating the XML file for the given location.

prepareBaseFile(input_folder::InputFolder)

Return the path to the base XML file for the given input folder.

prepareBaseRulesetsCollectionFile(input_folder::InputFolder)

Return the path to the base XML file for the given input folder.

prepareVariedInputFolder(location::Symbol, M::AbstractMonad)

Create the XML file for the location in the monad.

prepareVariedInputFolder(location::Symbol, sampling::Sampling)

Create the XML file for each monad in the sampling for the given location.

retrieveElement(xml_doc::XMLDocument, xml_path::Vector{<:AbstractString}; required::Bool=true)

Retrieve the element in the XML document that matches the given path.

If required is true, an error is thrown if the element is not found. Otherwise, nothing is returned if the element is not found.

retrieveElementError(xml_path::Vector{<:AbstractString}, path_element::String)

Throw an error if the element defined by xml_path is not found in the XML document, including the path element that caused the error.

ruleParameterName(name::String)

Return the short name of the varied parameter associated with a ruleset for the given name used in creating a DataFrame summary table.

sanitizePathElement(path_elements::String)

Disallow certain path elements to prevent security issues.

setSimpleContent(xml_doc::XMLDocument, xml_path::Vector{<:AbstractString}, new_value::Union{Int,Real,String})

Update the content of the element in the XML document that matches the given path with the new value. See retrieveElement.

Update the content of the element in the XML document that matches the given path with the new value. Validates that the element is terminal (has no child elements) before setting content. Throws AssertionError if the element has child elements.

setUpICCell(simulation::Simulation)

Return the path to the IC cell file for the given simulation, creating it if it needs to be generated from an XML file.

setUpICECM(simulation::Simulation)

Return the path to the IC ECM file for the given simulation, creating it if it needs to be generated from an XML file.

shortConfigVariationName(name::String)

Return the short name of the varied parameter in the configuration file for the given name used in creating a DataFrame summary table.

shortICCellVariationName(name::String)

Return the short name of the varied parameter in the IC cell file for the given name used in creating a DataFrame summary table.

shortICECMVariationName(name::String)

Return the short name of the varied parameter in the ECM file for the given name used in creating a DataFrame summary table.

shortIntracellularVariationName(name::String)

Return the short name of the varied parameter in the intracellular file for the given name used in creating a DataFrame summary table.

shortLocationVariationID(fieldname)

Return the short location variation ID name used in creating a DataFrame summary table.

Arguments

• fieldname: The field name to get the short location variation ID for. This can be a symbol or a string.

shortLocationVariationID(type::Type, fieldname::Union{String, Symbol})

Return (as a type) the short location variation ID name used in creating a DataFrame summary table.

shortRulesetsVariationName(name::String)

Return the short name of the varied parameter in the rulesets collection file for the given name used in creating a DataFrame summary table.

shortVariationName(location::Symbol, name::String)

Return the short name of the varied parameter for the given location and name used in creating a DataFrame summary table.

userParametersPath(tag::AbstractString)

Alias for userParameterPath.