morpheus.TcgaUtil = function () {

};

morpheus.TcgaUtil.DISEASE_STUDIES = {
	'LAML': 'Acute Myeloid Leukemia',
	'ACC': 'Adrenocortical carcinoma',
	'BLCA': 'Bladder Urothelial Carcinoma',
	'LGG': 'Brain Lower Grade Glioma',
	'BRCA': 'Breast invasive carcinoma',
	'CESC': 'Cervical squamous cell carcinoma and endocervical adenocarcinoma',
	'CHOL': 'Cholangiocarcinoma',
	'LCML': 'Chronic Myelogenous Leukemia',
	'COAD': 'Colon adenocarcinoma',
	'CNTL': 'Controls',
	'ESCA': 'Esophageal carcinoma ',
	'FPPP': 'FFPE Pilot Phase II',
	'GBM': 'Glioblastoma multiforme',
	'HNSC': 'Head and Neck squamous cell carcinoma',
	'KICH': 'Kidney Chromophobe',
	'KIRC': 'Kidney renal clear cell carcinoma',
	'KIRP': 'Kidney renal papillary cell carcinoma',
	'LIHC': 'Liver hepatocellular carcinoma',
	'LUAD': 'Lung adenocarcinoma',
	'LUSC': 'Lung squamous cell carcinoma',
	'DLBC': 'Lymphoid Neoplasm Diffuse Large B-cell Lymphoma',
	'MESO': 'Mesothelioma',
	'MISC': 'Miscellaneous',
	'OV': 'Ovarian serous cystadenocarcinoma',
	'PAAD': 'Pancreatic adenocarcinoma',
	'PCPG': 'Pheochromocytoma and Paraganglioma',
	'PRAD': 'Prostate adenocarcinoma',
	'READ': 'Rectum adenocarcinoma',
	'SARC': 'Sarcoma',
	'SKCM': 'Skin Cutaneous Melanoma',
	'STAD': 'Stomach adenocarcinoma',
	'TGCT': 'Testicular Germ Cell Tumors',
	'THYM': 'Thymoma',
	'THCA': 'Thyroid carcinoma',
	'UCS': 'Uterine Carcinosarcoma',
	'UCEC': 'Uterine Corpus Endometrial Carcinoma',
	'UVM': 'Uveal Melanoma',
	'KIPAN': 'Pan-Kidney Cohort',
	'COADREAD': 'Colonrectal adenocarcinoma',
	'GBMLGG': 'Glioma',
	'STES': 'Stomach and Esophageal Carcinoma'
};
morpheus.TcgaUtil.SAMPLE_TYPES = {
	'01': 'Primary solid Tumor',
	'02': 'Recurrent Solid Tumor',
	'03': 'Primary Blood Derived Cancer - Peripheral Blood',
	'04': 'Recurrent Blood Derived Cancer - Bone Marrow',
	'05': 'Additional - New Primary',
	'06': 'Metastatic',
	'07': 'Additional Metastatic',
	'08': 'Human Tumor Original Cells',
	'09': 'Primary Blood Derived Cancer - Bone Marrow',
	'10': 'Blood Derived Normal',
	'11': 'Solid Tissue Normal',
	'12': 'Buccal Cell Normal',
	'13': 'EBV Immortalized Normal',
	'14': 'Bone Marrow Normal',
	'20': 'Control Analyte',
	'40': 'Recurrent Blood Derived Cancer - Peripheral Blood',
	'50': 'Cell Lines',
	'60': 'Primary Xenograft Tissue',
	'61': 'Cell Line Derived Xenograft Tissue'
};

morpheus.TcgaUtil.barcode = function (s) {
	var tokens = s.split('-');
	var id = tokens[2];
	var sampleType;
	// e.g. TCGA-AC-A23H-01A-11D-A159-09
	if (tokens.length > 3) {
		sampleType = tokens[3];
		if (sampleType.length > 2) {
			sampleType = sampleType.substring(0, 2);
		}
		sampleType = morpheus.TcgaUtil.SAMPLE_TYPES[sampleType];
	} else {
		sampleType = morpheus.TcgaUtil.SAMPLE_TYPES['01'];
	}
	return {
		id: id.toLowerCase(),
		sampleType: sampleType
	};
};

morpheus.TcgaUtil.setIdAndSampleType = function (dataset) {
	var idVector = dataset.getColumnMetadata().get(0);
	var participantId = dataset.getColumnMetadata().add('participant_id');
	var sampleType = dataset.getColumnMetadata().add('sample_type');
	for (var i = 0, size = idVector.size(); i < size; i++) {
		var barcode = morpheus.TcgaUtil.barcode(idVector.getValue(i));
		idVector.setValue(i, barcode.id + '-' + barcode.sampleType);
		sampleType.setValue(i, barcode.sampleType);
		participantId.setValue(i, barcode.id);
	}
};

morpheus.TcgaUtil.getDataset = function (options) {
	var promises = [];
	var datasets = [];
	var returnDeferred = $.Deferred();

	if (options.mrna) {
		// id + type
		var mrna = $.Deferred();
		promises.push(mrna);
		new morpheus.TxtReader().read(options.mrna, function (err, dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}
			mrna.resolve();
		});
	}
	var sigGenesLines;
	if (options.mutation) {
		var mutation = $.Deferred();
		promises.push(mutation);
		new morpheus.MafFileReader().read(options.mutation, function (err,
																	  dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}
			mutation.resolve();
		});
		var sigGenesAnnotation = morpheus.Util.readLines(options.sigGenes);
		sigGenesAnnotation.done(function (lines) {
			sigGenesLines = lines;
		});
		promises.push(sigGenesAnnotation);
	}
	if (options.gistic) {
		var gistic = $.Deferred();
		promises.push(gistic);
		new morpheus.GisticReader().read(options.gistic,
			function (err, dataset) {
				if (err) {
					console.log('Error reading file:' + err);
				} else {
					datasets.push(dataset);
					morpheus.TcgaUtil.setIdAndSampleType(dataset);
				}
				gistic.resolve();
			});

	}
	if (options.gisticGene) {
		var gisticGene = $.Deferred();
		promises.push(gisticGene);

		new morpheus.TxtReader({
			dataColumnStart: 3

		}).read(options.gisticGene, function (err, dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}
			gisticGene.resolve();
		});

	}
	if (options.seg) {
		var seg = $.Deferred();
		promises.push(seg);
		new morpheus.SegTabReader().read(options.seg, function (err, dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}
			seg.resolve();
		});
	}
	if (options.rppa) {
		// id + type
		var rppa = $.Deferred();
		promises.push(rppa);

		new morpheus.TxtReader().read(options.rppa, function (err, dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}

			rppa.resolve();
		});

	}
	if (options.methylation) {
		// id + type
		var methylation = $.Deferred();
		promises.push(methylation);
		new morpheus.TxtReader({}).read(options.methylation, function (err,
																	   dataset) {
			if (err) {
				console.log('Error reading file:' + err);
			} else {
				datasets.push(dataset);
				morpheus.TcgaUtil.setIdAndSampleType(dataset);
			}
			methylation.resolve();
		});
	}

	var mrnaClustPromise = morpheus.Util.readLines(options.mrnaClust);
	promises.push(mrnaClustPromise);
	var sampleIdToClusterId;
	mrnaClustPromise.done(function (lines) {
		// SampleName cluster silhouetteValue
		// SampleName cluster silhouetteValue
		// TCGA-OR-A5J1-01 1 0.00648776228925048
		sampleIdToClusterId = new morpheus.Map();
		var lineNumber = 0;
		while (lines[lineNumber].indexOf('SampleName') !== -1) {
			lineNumber++;
		}
		var tab = /\t/;
		for (; lineNumber < lines.length; lineNumber++) {
			var tokens = lines[lineNumber].split(tab);
			var barcode = morpheus.TcgaUtil.barcode(tokens[0]);
			sampleIdToClusterId.set(barcode.id + '-' + barcode.sampleType, tokens[1]);
		}
	});
	var annotationCallbacks = [];
	var annotationDef = null;
	if (options.columnAnnotations) {
		annotationDef = morpheus.DatasetUtil.annotate({
			annotations: options.columnAnnotations,
			isColumns: true
		});
		promises.push(annotationDef);
		annotationDef.done(function (array) {
			annotationCallbacks = array;
		});
	}
	$.when.apply($, promises).then(
		function () {
			var datasetToReturn = null;
			if (datasets.length === 1) {
				var sourceName = datasets[0].getName();
				var sourceVector = datasets[0].getRowMetadata().add(
					'Source');
				for (var i = 0; i < sourceVector.size(); i++) {
					sourceVector.setValue(i, sourceName);
				}
				datasetToReturn = datasets[0];

			} else {
				var maxIndex = 0;
				var maxColumns = datasets[0].getColumnCount();
				// use dataset with most columns as the reference or
				// mutation data
				for (var i = 1; i < datasets.length; i++) {
					if (datasets[i].getColumnCount() > maxColumns) {
						maxColumns = datasets[i].getColumnCount();
						maxIndex = i;
					}
					if (datasets[i].getName() === 'mutations_merged.maf') {
						maxColumns = Number.MAX_VALUE;
						maxIndex = i;
					}
				}
				var datasetIndices = [];
				datasetIndices.push(maxIndex);
				for (var i = 0; i < datasets.length; i++) {
					if (i !== maxIndex) {
						datasetIndices.push(i);
					}
				}

				var joined = new morpheus.JoinedDataset(
					datasets[datasetIndices[0]],
					datasets[datasetIndices[1]], 'id', 'id');
				for (var i = 2; i < datasetIndices.length; i++) {
					joined = new morpheus.JoinedDataset(joined,
						datasets[datasetIndices[i]], 'id', 'id');
				}
				datasetToReturn = joined;
			}

			var clusterIdVector = datasetToReturn.getColumnMetadata().add(
				'mRNAseq_cluster');
			var idVector = datasetToReturn.getColumnMetadata().getByName(
				'id');
			for (var j = 0, size = idVector.size(); j < size; j++) {
				clusterIdVector.setValue(j, sampleIdToClusterId
				.get(idVector.getValue(j)));
			}
			// view in space of mutation sample ids only
			if (options.mutation) {
				var sourceToIndices = morpheus.VectorUtil
				.createValueToIndicesMap(datasetToReturn
				.getRowMetadata().getByName('Source'));
				var mutationDataset = new morpheus.SlicedDatasetView(
					datasetToReturn, sourceToIndices
					.get('mutations_merged.maf'));
				new morpheus.OpenFileTool()
				.annotate(sigGenesLines, mutationDataset, false,
					null, 'id', 'gene', ['q']);
				var qVector = mutationDataset.getRowMetadata().getByName(
					'q');
				var qValueVector = mutationDataset.getRowMetadata()
				.getByName('q_value');
				if (qValueVector == null) {
					qValueVector = mutationDataset.getRowMetadata().add(
						'q_value');
				}
				for (var i = 0, size = qValueVector.size(); i < size; i++) {
					qValueVector.setValue(i, qVector.getValue(i));
				}

				mutationDataset.getRowMetadata().remove(
					morpheus.MetadataUtil.indexOf(mutationDataset
					.getRowMetadata(), 'q'));
			}
			if (annotationDef) {
				annotationCallbacks.forEach(function (f) {
					f(datasetToReturn);
				});
			}
			returnDeferred.resolve(datasetToReturn);
		});
	return returnDeferred;
};