# Manuscript
# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to your installation

ARTICLE_FILE          = mutagenicity.md
PANDOC_SCHOLAR_PATH   = pandoc-scholar
OUTFILE_PREFIX        = mutagenicity
DEFAULT_EXTENSIONS    = latex pdf docx #odt epub html
PANDOC_WRITER_OPTIONS = --filter=pandoc-citeproc
#PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-citeproc
TEMPLATE_FILE_LATEX   = pandoc-scholar.latex

include $(PANDOC_SCHOLAR_PATH)/Makefile

# Lazar

LAZAR_DIR = ../lazar
LAZAR_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity
LAZAR_PADEL_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity-padel
LAZAR_SUMMARY_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/summaries
LAZAR_PADEL_SUMMARY_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/summaries
LAZAR_CONFUSION_MATRIX_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/confusion_matrices
LAZAR_PADEL_CONFUSION_MATRIX_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/confusion_matrices

# Experiments

SUMMARIES_DIR = 10-fold-crossvalidations/summaries
CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
R_CV_DIR = 10-fold-crossvalidations/R
TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow

#tables = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv

SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv $(SUMMARIES_DIR)/lazar-padel-all.csv $(SUMMARIES_DIR)/lazar-padel-high-confidence.csv

CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv

DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv

all: $(SUMMARIES) $(DATA) #$(tables)
export: $(DATA) 

# summaries

$(SUMMARIES_DIR)/%.csv: $(CONFUSION_MATRICES_DIR)/%.csv
	scripts/confusion-matrix-summary.rb $< > $@

# confusion matrices

## tensorflow
$(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.csv
	scripts/cv-tensorflow-confusion-matrix.rb $< > $@

$(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.csv
	scripts/cv-tensorflow-confusion-matrix.rb $< > $@

## R
$(CONFUSION_MATRICES_DIR)/R-SVM.csv: $(R_CV_DIR)/Sgl-Observations-SVM.csv
	scripts/cv-r-confusion-matrix.rb $< > $@

$(CONFUSION_MATRICES_DIR)/R-RF.csv: $(R_CV_DIR)/Sgl-Observations-RF.csv
	scripts/cv-r-confusion-matrix.rb $< > $@

$(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv
	scripts/cv-r-confusion-matrix.rb $< > $@

## lazar
$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CONFUSION_MATRIX_DIR)
	cp $</all $@

$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CONFUSION_MATRIX_DIR)
	cp $</high_confidence $@

$(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR)
	cp $</all $@

$(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR)
	cp $</high_confidence $@

# exports

data/mutagenicity-fingerprints.csv: $(LAZAR_DIR)/models/mutagenicity
	$(LAZAR_DIR)/bin/export-fingerprints.rb $< > $@

data/mutagenicity.csv: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
	cp $< > $@

data/mutagenicity.sdf: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
	$(LAZAR_DIR)/bin/export-sdf.rb $< > $@
	
# lazar models and crossvalidations

$(LAZAR_SUMMARY_DIR):
	make -C $(LAZAR_MODEL_DIR)

$(LAZAR_PADEL_SUMMARY_DIR):
	make -C $(LAZAR_PADEL_MODEL_DIR)