From 26de2a62133bae0546ee1263ba1cf10755a3ae6d Mon Sep 17 00:00:00 2001
From: IgorRodchenkov <rodche@gmail.com>
Date: Sun, 10 Mar 2024 15:46:41 -0400
Subject: [PATCH] Can now process compressed or not data files.

---
 README.md                                  |  1 +
 src/main/java/org/ctdbase/CtdToBiopax.java | 18 ++++++++++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index a55b15f..f620fe8 100644
--- a/README.md
+++ b/README.md
@@ -81,6 +81,7 @@ to run without any command line options to see the help text:
 	                          can use special values: 'defined', 'undefined', and 'null') [optional]
 	 -x,--interaction <arg>   structured chemical-gene interaction file (XML)
 	                          [optional]
+     Note: the input data files can be compressed, e.g. CTD_genes.csv.gz
 
 If you want to test the converter though, you can download small (old) example 
 files from [goal2_ctd_smallSampleInputFiles-20140702.zip](https://bitbucket.org/armish/gsoc14/downloads/goal2_ctd_smallSampleInputFiles-20140702.zip).
diff --git a/src/main/java/org/ctdbase/CtdToBiopax.java b/src/main/java/org/ctdbase/CtdToBiopax.java
index 639a0d6..32f894e 100644
--- a/src/main/java/org/ctdbase/CtdToBiopax.java
+++ b/src/main/java/org/ctdbase/CtdToBiopax.java
@@ -1,5 +1,6 @@
 package org.ctdbase;
 
+import org.apache.commons.lang3.StringUtils;
 import org.biopax.paxtools.model.level3.UtilityClass;
 import org.ctdbase.converter.CTDChemicalConverter;
 import org.ctdbase.converter.CTDGeneConverter;
@@ -11,14 +12,15 @@
 import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.model.BioPAXElement;
 import org.biopax.paxtools.model.Model;
-import org.biopax.paxtools.model.level3.EntityReference;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.Set;
+import java.util.zip.GZIPInputStream;
 
 public class CtdToBiopax {
     private static Logger log = LoggerFactory.getLogger(CtdToBiopax.class);
@@ -61,7 +63,7 @@ public static void main( String[] args ) {
                 }
                 Converter converter = new CTDInteractionConverter(taxonomy);
                 log.info("Option 'x'. Using " + converter.getClass().getSimpleName() + " to convert: " + fileName);
-                Model model = converter.convert(new FileInputStream(fileName));
+                Model model = converter.convert(inputDataStream(fileName));
                 merger.merge(finalModel, model);
             }
 
@@ -69,7 +71,7 @@ public static void main( String[] args ) {
                 String fileName = commandLine.getOptionValue("g");
                 Converter converter = new CTDGeneConverter();
                 log.info("Option 'g'. Using " + converter.getClass().getSimpleName() + " to convert: " + fileName);
-                Model model = converter.convert(new FileInputStream(fileName));
+                Model model = converter.convert(inputDataStream(fileName));
                 merger.merge(finalModel, model);
             }
 
@@ -77,7 +79,7 @@ public static void main( String[] args ) {
                 String fileName = commandLine.getOptionValue("c");
                 Converter converter = new CTDChemicalConverter();
                 log.info("Option 'c'. Using " + converter.getClass().getSimpleName() + " to convert: " + fileName);
-                Model model = converter.convert(new FileInputStream(fileName));
+                Model model = converter.convert(inputDataStream(fileName));
                 merger.merge(finalModel, model);
             }
 
@@ -103,4 +105,12 @@ public static void main( String[] args ) {
         }
     }
 
+    static InputStream inputDataStream(String fileName) throws IOException {
+        InputStream inputStream = new FileInputStream(fileName);
+        if (StringUtils.endsWith(fileName, ".gz")) {
+            inputStream = new GZIPInputStream(inputStream);
+        }
+        return inputStream;
+    }
+
 }