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

# 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
LAZAR_CV_DIR = 10-fold-crossvalidations/lazar

#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
# TODO lazar model/cv with PaDEL descriptors

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

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

# 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_CV_DIR)/lazar-crossvalidation.id
	scripts/cv-lazar-confusion-matrix.rb all $< > $@

$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
	scripts/cv-lazar-confusion-matrix.rb high-confidence $< > $@

# TODO lazar model/cv with PaDEL descriptors

# exports

data/mutagenicity-fingerprints.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
	scripts/export-fingerprints.rb $< > $@

data/mutagenicity.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
	scripts/export.rb $< training_csv > $@

data/mutagenicity.sdf: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
	scripts/export.rb $< sdf > $@
	
# lazar models and crossvalidations


$(LAZAR_CV_DIR)/lazar-crossvalidation.id: ../lazar/data/Mutagenicity-Salmonella_typhimurium.csv # adjust to match the location of your lazar libraries
	scripts/lazar-crossvalidation.rb $< > $@

# import
# TODO lazar model/cv with PaDEL descriptors

# cleanup

drop-database:
	scripts/drop-database.rb