Merge pull request #78 from drbergman/development

Development

Author: Daniel Bergman

Project.toml

@@ -1,7 +1,7 @@
 name = "pcvct"
 uuid = "3c374bc7-7384-4f83-8ca0-87b8c727e6ff"
 authors = ["Daniel Bergman <[email protected]> and contributors"]
-version = "0.0.12"
+version = "0.0.13"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

README.md

@@ -28,8 +28,6 @@ When an object `T <: AbstractTrial` is instantiated, immediately add it to the d
 If a simulation fails, remove it from the CSV without removing it from the database/output.
 
 # To dos
-- Figure out how to link pcvct verions to PhysiCell versions
-  - where does PhysiCell submodule fit in? Just for tests? Or for the whole package?
 - Rename for Julia registry. It will be so nice to have user Pkg.add("pcvct") and have it work.
   - PhysiCellVT.jl
   - PhysiVT.jl (possible confusion with the OpenVT project where VT = virtual tissue)

src/VCTClasses.jl

@@ -32,19 +32,19 @@ function loadCustomCode(S::AbstractSampling; force_recompile::Bool=false)
     if isdir(temp_custom_modules_dir)
         rm(temp_custom_modules_dir; force=true, recursive=true)
     end
-    path_to_input_custom_codes = joinpath(data_dir, "inputs", "custom_codes", S.folder_names.custom_code_folder)
+    path_to_input_custom_codes = joinpath(data_dir, "inputs", "custom_codes", S.inputs.custom_code.folder)
     cp(joinpath(path_to_input_custom_codes, "custom_modules"), temp_custom_modules_dir; force=true)
 
     cp(joinpath(path_to_input_custom_codes, "main.cpp"), joinpath(temp_physicell_dir, "main.cpp"), force=true)
     cp(joinpath(path_to_input_custom_codes, "Makefile"), joinpath(temp_physicell_dir, "Makefile"), force=true)
 
-    executable_name = baseToExecutable("project_ccid_$(S.folder_ids.custom_code_id)")
+    executable_name = baseToExecutable("project_ccid_$(S.inputs.custom_code.id)")
     cmd = `make -j 8 CC=$(PHYSICELL_CPP) PROGRAM_NAME=$(executable_name) CFLAGS=$(cflags)`
     # if Sys.isapple() # hacky way to say the -j flag works on my machine but not on the HPC
     #     cmd = `$cmd -j 20`
     # end
 
-    println("Compiling custom code for $(S.folder_names.custom_code_folder) with flags: $cflags")
+    println("Compiling custom code for $(S.inputs.custom_code.folder) with flags: $cflags")
 
     try
         cd(() -> run(pipeline(cmd; stdout=joinpath(path_to_input_custom_codes, "compilation.log"), stderr=joinpath(path_to_input_custom_codes, "compilation.err"))), temp_physicell_dir) # compile the custom code in the PhysiCell directory and return to the original directory
@@ -114,13 +114,13 @@ function compilerFlags(S::AbstractSampling)
         cflags *= " -D $(macro_flag)"
     end
 
-    recompile = recompile || !executableExists(S.folder_names.custom_code_folder) # last chance to recompile: do so if the executable does not exist
+    recompile = recompile || !executableExists(S.inputs.custom_code.folder) # last chance to recompile: do so if the executable does not exist
 
     return cflags, recompile, clean
 end
 
 function writePhysiCellCommitHash(S::AbstractSampling)
-    path_to_commit_hash = joinpath(data_dir, "inputs", "custom_codes", S.folder_names.custom_code_folder, "physicell_commit_hash.txt")
+    path_to_commit_hash = joinpath(data_dir, "inputs", "custom_codes", S.inputs.custom_code.folder, "physicell_commit_hash.txt")
     physicell_commit_hash = physiCellCommitHash()
     current_commit_hash = ""
     if isfile(path_to_commit_hash)
@@ -151,7 +151,7 @@ function addMacrosIfNeeded(S::AbstractSampling)
 end
 
 function addMacro(S::AbstractSampling, macro_name::String)
-    path_to_macros = joinpath(data_dir, "inputs", "custom_codes", S.folder_names.custom_code_folder, "macros.txt")
+    path_to_macros = joinpath(data_dir, "inputs", "custom_codes", S.inputs.custom_code.folder, "macros.txt")
     open(path_to_macros, "a") do f
         println(f, macro_name)
     end
@@ -162,7 +162,7 @@ function addPhysiECMIfNeeded(S::AbstractSampling)
         # if the custom codes folder for the sampling already has the macro, then we don't need to do anything
         return
     end
-    if S.folder_ids.ic_ecm_id != -1
+    if S.inputs.ic_ecm.id != -1
         # if this sampling is providing an ic file for ecm, then we need to add the macro
         addMacro(S, "ADDON_PHYSIECM")
         return
@@ -176,7 +176,7 @@ function addPhysiECMIfNeeded(S::AbstractSampling)
 end
 
 function isPhysiECMInConfig(M::AbstractMonad)
-    path_to_xml = joinpath(data_dir, "inputs", "configs", M.folder_names.config_folder, "config_variations", "config_variation_$(M.variation_ids.config).xml")
+    path_to_xml = joinpath(data_dir, "inputs", "configs", M.inputs.config.folder, "config_variations", "config_variation_$(M.variation_ids.config).xml")
     xml_doc = openXML(path_to_xml)
     xml_path = ["microenvironment_setup", "ecm_setup"]
     ecm_setup_element = retrieveElement(xml_doc, xml_path; required=false)
@@ -198,7 +198,7 @@ function isPhysiECMInConfig(sampling::Sampling)
 end
 
 function readMacrosFile(S::AbstractSampling)
-    path_to_macros = joinpath(data_dir, "inputs", "custom_codes", S.folder_names.custom_code_folder, "macros.txt")
+    path_to_macros = joinpath(data_dir, "inputs", "custom_codes", S.inputs.custom_code.folder, "macros.txt")
     if !isfile(path_to_macros)
         return []
     end

src/VCTCompilation.jl

@@ -75,17 +75,17 @@ end
 ################## Configuration Functions ##################
 
 function loadConfiguration(M::AbstractMonad)
-    path_to_xml = joinpath(data_dir, "inputs", "configs", M.folder_names.config_folder, "config_variations", "config_variation_$(M.variation_ids.config).xml")
+    path_to_xml = joinpath(data_dir, "inputs", "configs", M.inputs.config.folder, "config_variations", "config_variation_$(M.variation_ids.config).xml")
     if isfile(path_to_xml)
         return
     end
     mkpath(dirname(path_to_xml))
-    path_to_xml_src = joinpath(data_dir, "inputs", "configs", M.folder_names.config_folder, "PhysiCell_settings.xml")
+    path_to_xml_src = joinpath(data_dir, "inputs", "configs", M.inputs.config.folder, "PhysiCell_settings.xml")
     cp(path_to_xml_src, path_to_xml, force=true)
 
     xml_doc = openXML(path_to_xml)
     query = constructSelectQuery("config_variations", "WHERE config_variation_id=$(M.variation_ids.config);")
-    variation_row = queryToDataFrame(query; db=configDB(M.folder_names.config_folder), is_row=true)
+    variation_row = queryToDataFrame(query; db=configDB(M.inputs.config.folder), is_row=true)
     for column_name in names(variation_row)
         if column_name == "config_variation_id"
             continue
@@ -106,12 +106,12 @@ function loadConfiguration(sampling::Sampling)
 end
 
 function loadRulesets(M::AbstractMonad)
-    if M.variation_ids.rulesets == -1 # no rules being used
+    if M.variation_ids.rulesets_collection == -1 # no rules being used
         return
     end
-    path_to_rulesets_collections_folder = joinpath(data_dir, "inputs", "rulesets_collections", M.folder_names.rulesets_collection_folder)
-    path_to_rulesets_xml = joinpath(path_to_rulesets_collections_folder, "rulesets_collections_variations", "rulesets_variation_$(M.variation_ids.rulesets).xml")
-    if isfile(path_to_rulesets_xml) # already have the rulesets variation created
+    path_to_rulesets_collections_folder = joinpath(data_dir, "inputs", "rulesets_collections", M.inputs.rulesets_collection.folder)
+    path_to_rulesets_xml = joinpath(path_to_rulesets_collections_folder, "rulesets_collections_variations", "rulesets_variation_$(M.variation_ids.rulesets_collection).xml")
+    if isfile(path_to_rulesets_xml) # already have the rulesets_collection variation created
         return
     end
     mkpath(dirname(path_to_rulesets_xml)) # ensure the directory exists
@@ -124,11 +124,11 @@ function loadRulesets(M::AbstractMonad)
     end
 
     xml_doc = parse_file(path_to_base_xml)
-    if M.variation_ids.rulesets != 0 # only update if not using the base variation for the ruleset
-        query = constructSelectQuery("rulesets_variations", "WHERE rulesets_variation_id=$(M.variation_ids.rulesets);")
+    if M.variation_ids.rulesets_collection != 0 # only update if not using the base variation for the ruleset
+        query = constructSelectQuery("rulesets_collection_variations", "WHERE rulesets_collection_variation_id=$(M.variation_ids.rulesets_collection);")
         variation_row = queryToDataFrame(query; db=rulesetsCollectionDB(M), is_row=true)
         for column_name in names(variation_row)
-            if column_name == "rulesets_variation_id"
+            if column_name == "rulesets_collection_variation_id"
                 continue
             end
             xml_path = columnNameToXMLPath(column_name)
@@ -141,10 +141,10 @@ function loadRulesets(M::AbstractMonad)
 end
 
 function loadICCells(M::AbstractMonad)
-    if M.folder_ids.ic_cell_id == -1 # no ic cells being used
+    if M.inputs.ic_cell.id == -1 # no ic cells being used
         return
     end
-    path_to_ic_cells_folder = joinpath(data_dir, "inputs", "ics", "cells", M.folder_names.ic_cell_folder)
+    path_to_ic_cells_folder = joinpath(data_dir, "inputs", "ics", "cells", M.inputs.ic_cell.folder)
     if isfile(joinpath(path_to_ic_cells_folder, "cells.csv")) # ic already given by cells.csv
         return
     end
@@ -158,7 +158,7 @@ function loadICCells(M::AbstractMonad)
     xml_doc = parse_file(path_to_base_xml)
     if M.variation_ids.ic_cell != 0 # only update if not using the base variation for the ic cells
         query = constructSelectQuery("ic_cell_variations", "WHERE ic_cell_variation_id=$(M.variation_ids.ic_cell);")
-        variation_row = queryToDataFrame(query; db=icCellDB(M.folder_names.ic_cell_folder), is_row=true)
+        variation_row = queryToDataFrame(query; db=icCellDB(M.inputs.ic_cell.folder), is_row=true)
         for column_name in names(variation_row)
             if column_name == "ic_cell_variation_id"
                 continue
@@ -173,8 +173,8 @@ function loadICCells(M::AbstractMonad)
 end
 
 function pathToICCell(simulation::Simulation)
-    @assert simulation.folder_ids.ic_cell_id != -1 "No IC cell variation being used" # we should have already checked this before calling this function
-    path_to_ic_cell_folder = joinpath(data_dir, "inputs", "ics", "cells", simulation.folder_names.ic_cell_folder)
+    @assert simulation.inputs.ic_cell.id != -1 "No IC cell variation being used" # we should have already checked this before calling this function
+    path_to_ic_cell_folder = joinpath(data_dir, "inputs", "ics", "cells", simulation.inputs.ic_cell.folder)
     if isfile(joinpath(path_to_ic_cell_folder, "cells.csv")) # ic already given by cells.csv
         return joinpath(path_to_ic_cell_folder, "cells.csv")
     end
@@ -291,7 +291,7 @@ function simpleConfigVariationNames(name::String)
 end
 
 function simpleRulesetsVariationNames(name::String)
-    if name == "rulesets_variation_id"
+    if name == "rulesets_collection_variation_id"
         return "RulesVarID"
     elseif startswith(name, "hypothesis_ruleset")
         return getRuleParameterName(name)