From d0f9467fc350cf9fb707a525c310e8bd77018af4 Mon Sep 17 00:00:00 2001 From: Joshua Klein Date: Sat, 31 Aug 2024 18:23:40 -0400 Subject: [PATCH] Regenerate test bundle --- examples/chinese_hamster_hcd_selected_head.mzlb.txt | 2 +- mzspeclib/backends/json.py | 6 ++++-- mzspeclib/backends/msp.py | 3 ++- mzspeclib/backends/text.py | 3 ++- mzspeclib/backends/utils.py | 3 ++- tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt | 2 +- 6 files changed, 12 insertions(+), 7 deletions(-) diff --git a/examples/chinese_hamster_hcd_selected_head.mzlb.txt b/examples/chinese_hamster_hcd_selected_head.mzlb.txt index 1490058..6948505 100644 --- a/examples/chinese_hamster_hcd_selected_head.mzlb.txt +++ b/examples/chinese_hamster_hcd_selected_head.mzlb.txt @@ -1,4 +1,4 @@ - + MS:1003186|library format version=1.0 MS:1003188|library name=examples/chinese_hamster_hcd_selected_head diff --git a/mzspeclib/backends/json.py b/mzspeclib/backends/json.py index 933b22e..7b6138e 100644 --- a/mzspeclib/backends/json.py +++ b/mzspeclib/backends/json.py @@ -509,8 +509,10 @@ def flush(self): json.dump(spectra, self.handle) def close(self): - self.flush() - self.handle.close() + if not self.handle.closed: + self.flush() + self.handle.close() + def format_spectrum(spectrum: Spectrum, pretty_print=True, **kwargs) -> str: diff --git a/mzspeclib/backends/msp.py b/mzspeclib/backends/msp.py index c734886..0024804 100644 --- a/mzspeclib/backends/msp.py +++ b/mzspeclib/backends/msp.py @@ -2146,4 +2146,5 @@ def _write_peaks(self, spectrum: Spectrum): self.handle.write(f'{peak[0]:0.4f}\t{peak[1]:0.4f}\t"{annot}"\n') def close(self): - self.handle.close() + if not self.handle.closed: + self.handle.close() diff --git a/mzspeclib/backends/text.py b/mzspeclib/backends/text.py index 967c512..9128c01 100644 --- a/mzspeclib/backends/text.py +++ b/mzspeclib/backends/text.py @@ -1020,7 +1020,8 @@ def write_cluster(self, cluster: SpectrumCluster): self.handle.write("\n") def close(self): - self.handle.close() + if not self.handle.closed: + self.handle.close() def format_aggregation(value: Union[numbers.Number, str]) -> str: diff --git a/mzspeclib/backends/utils.py b/mzspeclib/backends/utils.py index d93d730..fabebb1 100644 --- a/mzspeclib/backends/utils.py +++ b/mzspeclib/backends/utils.py @@ -368,8 +368,9 @@ def close(self): self.buffer.close() return self.stream.close() + @property def closed(self): - return self.stream.closed() + return self.stream.closed def seekable(self): return True diff --git a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt index b1b15ac..3c128ca 100644 --- a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt +++ b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt @@ -1,4 +1,4 @@ - + MS:1003186|library format version=1.0 MS:1003188|library name=tests/test_data/chinese_hamster_hcd_selected_head