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|
Author: Michael R. Crusoe <crusoe@gmail.com>
Description: Remove tests referencing missing tests data
Forwarded: not-needed
Drop this patch once upstream ships the "tests" data in their crate.
--- needletail.orig/src/parser/fastq.rs
+++ needletail/src/parser/fastq.rs
@@ -601,29 +601,4 @@
let e = rec.unwrap_err();
assert_eq!(e.kind, ParseErrorKind::UnequalLengths);
}
-
- // https://github.com/onecodex/needletail/pull/36
- #[test]
- fn test_bad_headers() {
- let mut reader = Reader::from_path("tests/data/bad_header.fastq").unwrap();
- let rec = reader.next().unwrap();
- assert!(rec.is_ok());
- let rec2 = reader.next().unwrap();
- let e = rec2.unwrap_err();
- // Ideally this would not be UnexpectedEnd since we know it's an invalid record
- // but that's for another day
- assert_eq!(e.kind, ParseErrorKind::UnexpectedEnd);
- }
-
- // https://github.com/onecodex/needletail/pull/39
- #[test]
- fn test_fastq_with_random_tsv_inside() {
- let mut reader = Reader::from_path("tests/data/random_tsv.fq").unwrap();
- let rec = reader.next().unwrap();
- assert!(rec.is_ok());
- let rec2 = reader.next().unwrap();
- let e = rec2.unwrap_err();
- // It errors when it tries to validate the separator line that needs to start with `+`
- assert_eq!(e.kind, ParseErrorKind::InvalidSeparator);
- }
}
--- needletail.orig/tests/test_compressed.rs
+++ needletail/tests/test_compressed.rs
@@ -37,10 +37,4 @@
}
}
-#[cfg(not(feature = "compression"))]
-#[test]
-fn errors_on_compressed_files() {
- for p in &TEST_FILES {
- assert!(parse_fastx_file(p).is_err());
- }
-}
+
--- needletail.orig/tests/test_stdin.rs
+++ needletail/tests/test_stdin.rs
@@ -3,138 +3,4 @@
use assert_cmd::prelude::*;
use predicates::str::contains;
-#[cfg(feature = "compression")]
-#[test]
-fn test_stdin_gz() {
- // Generated with `echo ">id1\nAGTCGTCA" | gzip -c | xxd -i`
- let input: &[u8] = &[
- 0x1f, 0x8b, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x03, 0xb3, 0xcb, 0x4c, 0x31, 0xe4,
- 0x72, 0x74, 0x0f, 0x71, 0x06, 0x22, 0x47, 0x2e, 0x00, 0x9e, 0x3a, 0x32, 0x8c, 0x0e, 0x00,
- 0x00, 0x00,
- ];
- let mut file = tempfile::NamedTempFile::new().unwrap();
- file.write_all(input).unwrap();
- file.flush().unwrap();
- file.seek(SeekFrom::Start(0)).unwrap();
- escargot::CargoBuild::new()
- .example("stdin_pipe")
- .current_release()
- .current_target()
- .run()
- .unwrap()
- .command()
- .stdin(file.into_file())
- .assert()
- .success()
- .stdout(contains("There are 8 bases in your file"))
- .stdout(contains("There are 0 AAAAs in your file"));
-}
-
-#[cfg(feature = "compression")]
-#[test]
-fn test_stdin_xz() {
- // Generated with `echo ">id1\nAGTCGTCA" | xz -c | xxd -i`
- let input: &[u8] = &[
- 0xfd, 0x37, 0x7a, 0x58, 0x5a, 0x00, 0x00, 0x04, 0xe6, 0xd6, 0xb4, 0x46, 0x02, 0x00, 0x21,
- 0x01, 0x16, 0x00, 0x00, 0x00, 0x74, 0x2f, 0xe5, 0xa3, 0x01, 0x00, 0x0d, 0x3e, 0x69, 0x64,
- 0x31, 0x0a, 0x41, 0x47, 0x54, 0x43, 0x47, 0x54, 0x43, 0x41, 0x0a, 0x00, 0x00, 0x00, 0x12,
- 0x0f, 0x91, 0x75, 0xef, 0x7b, 0x63, 0x17, 0x00, 0x01, 0x26, 0x0e, 0x08, 0x1b, 0xe0, 0x04,
- 0x1f, 0xb6, 0xf3, 0x7d, 0x01, 0x00, 0x00, 0x00, 0x00, 0x04, 0x59, 0x5a,
- ];
- let mut file = tempfile::NamedTempFile::new().unwrap();
- file.write_all(input).unwrap();
- file.flush().unwrap();
- file.seek(SeekFrom::Start(0)).unwrap();
-
- escargot::CargoBuild::new()
- .example("stdin_pipe")
- .current_release()
- .current_target()
- .run()
- .unwrap()
- .command()
- .stdin(file.into_file())
- .assert()
- .success()
- .stdout(contains("There are 8 bases in your file"))
- .stdout(contains("There are 0 AAAAs in your file"));
-}
-
-#[cfg(feature = "compression")]
-#[test]
-fn test_stdin_bzip() {
- // Generated with `echo ">id1\nAGTCGTCA" | bzip2 -c | xxd -i`
- let input: &[u8] = &[
- 0x42, 0x5a, 0x68, 0x39, 0x31, 0x41, 0x59, 0x26, 0x53, 0x59, 0x9f, 0x9d, 0xf9, 0xa2, 0x00,
- 0x00, 0x01, 0xcf, 0x00, 0x00, 0x10, 0x20, 0x01, 0x28, 0x80, 0x04, 0x00, 0x04, 0x20, 0x20,
- 0x00, 0x22, 0x0c, 0x9a, 0x64, 0x20, 0xc9, 0x88, 0x21, 0x95, 0x8e, 0x82, 0x75, 0x27, 0x8b,
- 0xb9, 0x22, 0x9c, 0x28, 0x48, 0x4f, 0xce, 0xfc, 0xd1, 0x00,
- ];
- let mut file = tempfile::NamedTempFile::new().unwrap();
- file.write_all(input).unwrap();
- file.flush().unwrap();
- file.seek(SeekFrom::Start(0)).unwrap();
-
- escargot::CargoBuild::new()
- .example("stdin_pipe")
- .current_release()
- .current_target()
- .run()
- .unwrap()
- .command()
- .stdin(file.into_file())
- .assert()
- .success()
- .stdout(contains("There are 8 bases in your file"))
- .stdout(contains("There are 0 AAAAs in your file"));
-}
-
-#[cfg(feature = "compression")]
-#[test]
-fn test_stdin_zstd() {
- // Generated with `echo ">id1\nAGTCGTCA" | zstd -c | xxd -i`
- let input: &[u8] = &[
- 0x28, 0xb5, 0x2f, 0xfd, 0x04, 0x58, 0x71, 0x00, 0x00, 0x3e, 0x69, 0x64, 0x31, 0x0a, 0x41,
- 0x47, 0x54, 0x43, 0x47, 0x54, 0x43, 0x41, 0x0a, 0x52, 0x9d, 0x37, 0x8d,
- ];
- let mut file = tempfile::NamedTempFile::new().unwrap();
- file.write_all(input).unwrap();
- file.flush().unwrap();
- file.seek(SeekFrom::Start(0)).unwrap();
-
- escargot::CargoBuild::new()
- .example("stdin_pipe")
- .current_release()
- .current_target()
- .run()
- .unwrap()
- .command()
- .stdin(file.into_file())
- .assert()
- .success()
- .stdout(contains("There are 8 bases in your file"))
- .stdout(contains("There are 0 AAAAs in your file"));
-}
-
-#[test]
-fn test_stdin_no_compression() {
- let input: &[u8] = b">id1\nAGTCGTCA";
- let mut file = tempfile::NamedTempFile::new().unwrap();
- file.write_all(input).unwrap();
- file.flush().unwrap();
- file.seek(SeekFrom::Start(0)).unwrap();
-
- escargot::CargoBuild::new()
- .example("stdin_pipe")
- .current_release()
- .current_target()
- .run()
- .unwrap()
- .command()
- .stdin(file.into_file())
- .assert()
- .success()
- .stdout(contains("There are 8 bases in your file"))
- .stdout(contains("There are 0 AAAAs in your file"));
-}
|
