Fix readAllBytes with http files (#5202)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Aug 5, 2024 · 7e90ce6 · 7e90ce6
1 parent e7a879d
commit 7e90ce6
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Showing 2 changed files with 8 additions and 18 deletions.
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
@@ -255,7 +255,7 @@ abstract class XFileSystemProvider extends FileSystemProvider {
  int read(ByteBuffer buffer) throws IOException {
  def data=0
  int len=0
- while( len<buffer.capacity() && (data=stream.read())!=-1 ) {
+ while( buffer.hasRemaining() && (data=stream.read())!=-1 ) {
  buffer.put((byte)data)
  len++
  }

diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy
@@ -113,7 +113,7 @@ class HttpFilesTests extends Specification {
  then:
  lines.size()>0
  lines[0].startsWith('<!DOCTYPE html><html lang="en">')
-
+ 
  }
 
  def 'should check file properties' () {
@@ -190,27 +190,17 @@ class HttpFilesTests extends Specification {
  @IgnoreIf({System.getenv('NXF_SMOKE')})
  def 'should read lines' () {
  given:
- def path = Paths.get(new URI('ftp://ftp.ncbi.nlm.nih.gov/robots.txt'))
-
+ def uri = new URI('http://www.nextflow.io/index.html')
  when:
- def lines = Files.readAllLines(path, Charset.forName('UTF-8'))
+ def path = Paths.get(uri)
  then:
- lines[0] == 'User-agent: *'
- lines[1] == 'Disallow: /'
- }
-
- @IgnoreIf({System.getenv('NXF_SMOKE')})
- def 'should read all bytes' ( ) {
- given:
- def path = Paths.get(new URI('ftp://ftp.ncbi.nlm.nih.gov/robots.txt'))
+ path instanceof XPath
 
  when:
- def bytes = Files.readAllBytes(path)
- def lines = new String(bytes).readLines()
+ def str = new String(Files.readAllBytes(path), Charset.forName('UTF-8'))
  then:
- lines[0] == 'User-agent: *'
- lines[1] == 'Disallow: /'
-
+ str.size()>0
+ str.startsWith('<!DOCTYPE html><html lang="en">')
  }
 
  def 'should read with a newByteChannel' () {