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Merge pull request #47 from stevekm/fastqc-unit-test

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move md5 function to lib dir and symlink to fastqc test dir, rename m…
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Phil Ewels 2020-07-23 11:46:10 +02:00 committed by GitHub
commit 6dfb9f02c9
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3 changed files with 39 additions and 38 deletions
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34
lib/checksum.groovy Normal file
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@ -0,0 +1,34 @@
import java.security.MessageDigest
private static String getMD5(File file) throws IOException
{
// https://howtodoinjava.com/java/io/how-to-generate-sha-or-md5-file-checksum-hash-in-java/
//Get file input stream for reading the file content
FileInputStream fis = new FileInputStream(file);
//Create byte array to read data in chunks
byte[] byteArray = new byte[1024];
int bytesCount = 0;
//Read file data and update in message digest
def digest = MessageDigest.getInstance("MD5")
while ((bytesCount = fis.read(byteArray)) != -1) {
digest.update(byteArray, 0, bytesCount);
};
//close the stream; We don't need it now.
fis.close();
//Get the hash's bytes
byte[] bytes = digest.digest();
//This bytes[] has bytes in decimal format;
//Convert it to hexadecimal format
StringBuilder sb = new StringBuilder();
for(int i=0; i< bytes.length ;i++)
{
sb.append(Integer.toString((bytes[i] & 0xff) + 0x100, 16).substring(1));
}
//return complete hash
return sb.toString();
}

1
software/fastqc/test/lib Symbolic link
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@ -0,0 +1 @@
../../../lib

42
software/fastqc/test/main.nf
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@ -1,5 +1,5 @@
#!/usr/bin/env nextflow
import java.security.MessageDigest
import checksum
nextflow.preview.dsl = 2
params.out_dir = "test_output"
@ -8,40 +8,6 @@ params.publish_dir_mode = "copy"
include { FASTQC } from '../main.nf'
private static String getFileChecksum(MessageDigest digest, File file) throws IOException
{
// https://howtodoinjava.com/java/io/how-to-generate-sha-or-md5-file-checksum-hash-in-java/
//Get file input stream for reading the file content
FileInputStream fis = new FileInputStream(file);
//Create byte array to read data in chunks
byte[] byteArray = new byte[1024];
int bytesCount = 0;
//Read file data and update in message digest
while ((bytesCount = fis.read(byteArray)) != -1) {
digest.update(byteArray, 0, bytesCount);
};
//close the stream; We don't need it now.
fis.close();
//Get the hash's bytes
byte[] bytes = digest.digest();
//This bytes[] has bytes in decimal format;
//Convert it to hexadecimal format
StringBuilder sb = new StringBuilder();
for(int i=0; i< bytes.length ;i++)
{
sb.append(Integer.toString((bytes[i] & 0xff) + 0x100, 16).substring(1));
}
//return complete hash
return sb.toString();
}
/**
* Test if FASTQC runs with single-end data
*/
@ -52,7 +18,7 @@ workflow test_single_end {
// test that the output looks as expected
FASTQC.out.html.map { name, is_single_end, html_file ->
html_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_file}"));
html_hash = checksum.getMD5(new File("${html_file}"));
assert name == "test_single_end"
assert is_single_end == true
@ -82,8 +48,8 @@ workflow test_paired_end {
html_r1 = html_files[0]
html_r2 = html_files[1]
html_r1_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_r1}"));
html_r2_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_r2}"));
html_r1_hash = checksum.getMD5(new File("${html_r1}"));
html_r2_hash = checksum.getMD5(new File("${html_r2}"));
assert name == "test_R"
assert is_single_end == false