From 504d7d6af68173fd1591b786c804822dfae6c7ea Mon Sep 17 00:00:00 2001
From: jgould <jgould@broadinstitute.org>
Date: Fri, 15 Apr 2016 16:24:01 -0400
Subject: [PATCH] convert to string arrays

---
 src/io/gct_reader.js        | 11 +++--------
 src/matrix/metadata_util.js | 33 +++++++++++++++------------------
 src/matrix/vector_util.js   | 25 +++++++++++++++++++++++++
 3 files changed, 43 insertions(+), 26 deletions(-)

diff --git a/src/io/gct_reader.js b/src/io/gct_reader.js
index dbc969f..fc9702f 100644
--- a/src/io/gct_reader.js
+++ b/src/io/gct_reader.js
@@ -183,14 +183,9 @@ morpheus.GctReader.prototype = {
 			throw new Error('Missing data rows');
 		}
 
-		for (var i = 1, count = dataset.getRowMetadata().getMetadataCount(); i < count; i++) {
-			morpheus.VectorUtil.maybeConvertStringToNumber(dataset
-					.getRowMetadata().get(i));
-		}
-		for (var i = 1, count = dataset.getColumnMetadata().getMetadataCount(); i < count; i++) {
-			morpheus.VectorUtil.maybeConvertStringToNumber(dataset
-					.getColumnMetadata().get(i));
-		}
+		morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(), 1);
+		morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),
+				1);
 		return dataset;
 	}
 };
diff --git a/src/matrix/metadata_util.js b/src/matrix/metadata_util.js
index a522dac..be75aba 100644
--- a/src/matrix/metadata_util.js
+++ b/src/matrix/metadata_util.js
@@ -317,6 +317,8 @@ morpheus.MetadataUtil.indexOf = function(metadataModel, name) {
 	return -1;
 };
 
+morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS = [ 'target', 'moa' ];
+
 morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS = new morpheus.Set();
 [ 'pr_analyte_id', 'pr_gene_title', 'pr_gene_id', 'pr_analyte_num',
 		'pr_bset_id', 'pr_lua_id', 'pr_pool_id', 'pr_is_bing', 'pr_is_inf',
@@ -329,24 +331,19 @@ morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS = new morpheus.Set();
 		'count_cv', 'provenance_code' ].forEach(function(name) {
 	morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.add(name);
 });
-morpheus.MetadataUtil.DEFAULT_FIELDS_TO_SHOW = {
-	'cell_id' : true,
-	'pert_idose' : true,
-	'pert_itime' : true,
-	'Id' : true,
-	'Name' : true,
-	'ID' : true,
-	'pr_id' : true,
-	'id' : true,
-	'pr_gene_symbol' : true,
-	'pr_is_lm' : true,
-	'is_lm' : true,
-	'pert_id' : true,
-	'pert_iname' : true,
-	'pert_desc' : true,
-	'Description' : true,
-	'gene_space' : true,
-	'pert_type' : true
+
+morpheus.MetadataUtil.maybeConvertStrings = function(metadata,
+		metadataStartIndex) {
+	for (var i = metadataStartIndex, count = metadata.getMetadataCount(); i < count; i++) {
+		morpheus.VectorUtil.maybeConvertStringToNumber(metadata.get(i));
+	}
+	morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS.forEach(function(field) {
+		if (metadata.getByName(field)) {
+			morpheus.VectorUtil.maybeConvertToStringArray(metadata
+					.getByName(field), ',');
+		}
+	});
+
 };
 morpheus.MetadataUtil.copy = function(src, dest) {
 	if (src.getItemCount() != dest.getItemCount()) {
diff --git a/src/matrix/vector_util.js b/src/matrix/vector_util.js
index 53c3871..7355ff2 100644
--- a/src/matrix/vector_util.js
+++ b/src/matrix/vector_util.js
@@ -39,6 +39,30 @@ morpheus.VectorUtil.createValueToCountMap = function(vector) {
 	}
 	return map;
 };
+morpheus.VectorUtil.maybeConvertToStringArray = function(vector, delim) {
+	var newValues = [];
+	var regex = new RegExp(delim);
+	var found = false;
+	for (var i = 0, nrows = vector.size(); i < nrows; i++) {
+		var s = vector.getValue(i);
+		if (s != null) {
+			var tokens = s.split(regex);
+			newValues.push(tokens);
+			if (!found && tokens.length > 1) {
+				found = true;
+			}
+		}
+
+	}
+	if (found) {
+		for (var i = 0, nrows = newValues.length; i < nrows; i++) {
+			vector.setValue(i, newValues[i]);
+		}
+	}
+	vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE, '[string]');
+	return found;
+};
+
 morpheus.VectorUtil.maybeConvertStringToNumber = function(vector) {
 	var newValues = [];
 
@@ -54,6 +78,7 @@ morpheus.VectorUtil.maybeConvertStringToNumber = function(vector) {
 	for (var i = 0, nrows = newValues.length; i < nrows; i++) {
 		vector.setValue(i, newValues[i]);
 	}
+	vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE, 'number');
 	return true;
 };
 morpheus.VectorUtil.createValuesToIndicesMap = function(vectors) {
-- 
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